gmod-ajax — JBrowse list

Re: [Gmod-ajax] JBrowse XML parsing errors

[Vaneet L. <van...@uc...>]

Thanks Colin, that's good to know.

Vaneet
________________________________
From: Colin <col...@gm...>
Sent: June 1, 2022 4:43 PM
To: Vaneet Lotay <van...@uc...>
Cc: gmo...@li... <gmo...@li...>
Subject: Re: [Gmod-ajax] JBrowse XML parsing errors

[△EXTERNAL]


Hi Vaneet,

This console log message is just a browser specific thing with Firefox, but as far as I know does not indicate anything is wrong. It is just something Firefox says when a .conf file is downloaded, but the .conf file is otherwise interpreted fine by the JBrowse code itself. I think you can ignore the message


-Colin

On Wed, Jun 1, 2022 at 11:59 AM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hi,

I attached a screenshot of the XML parsing errors from the console of my Firefox browser, which I'm a little confused about.  I checked the actual configuration files that these errors denote, and I don't see anything wrong or any hidden characters that are there on the first line.  I don't think these are file specific though as no matter what genome I switch to in JBrowse I see the same errors, that is those genomes for which I have an extra configuration file for functions that's named 'functions.conf'.  The jbrowse.conf error always appears.  I don't see any visible problem on the browser tracks that results from these errors but I just want to eliminate them to make sure.

After looking at the JBrowse 1 troubleshooting page, I took the suggestion to install the libexpat1-dev package and then rerun the setup.sh script, but errors are still there on Firefox.  If I load the page in Microsoft Edge browser, I don't see the errors there, so I'm wondering if it's browser specific? Is anyone aware of any fixes for this specific issue?

Thanks,

Vaneet
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Re: [Gmod-ajax] Dataset selector in apollo

[Colin <col...@gm...>]

>From my quick testing, I think the order in which they are specified in the
jbrowse.conf is the order in which they will be listed in the Genome menu.
I cannot guarantee this would be the same situation for Apollo and am not
aware of any custom config to help this ordering in Apollo.

If you have an example jbrowse.conf config where it doesn't seem to be
doing this in JBrowse though, feel free to post


-Colin

On Wed, Jun 1, 2022 at 12:30 PM Justin Elser <jus...@or...>
wrote:

> So, this is hopefully an easy question, and I may have just missed it in
> the documentation, but is there a way to change the order in which the
> datasets show up in the genome selector?
>
> It looks like they get added in the order in which they were added, or
> possibly alphanumeric by dataset_id?
>
> In the below screenshot, I'd like Minghui63 to be between Liu Xu and
> Nagina 22, but since it is the last one I added, it shows up last. I have
> it where I want it in the jbrowse.conf file, but it still shows up last. I
> don't totally want them in alphabetical order, as I would like Nipponbare
> to be first.
>
> Is it possible to change this?
>
> Thanks,
> Justin
>
> On 5/26/22 2:05 PM, Colin wrote:
>
> [This email originated from outside of OSU. Use caution with links and
> attachments.]
> >Everything works as expected now! I see both Nipponbare and ARC in the
> "Genome" dropdown, and apollo is showing all data.
>
> Excellent:)
>
> >So, I guess apollo is only using the numeric ID for the dataset instead
> of using what I tried to set the dataset id? In other words, if I had
> [datasets.nipponbare] in jbrowse.conf and dataset_id=nipponbare in
> data/nipponbare/tracks.conf, that is fine for jbrowse, but apollo is only
> using it's internal ID of 34?
>
> You can inspect the database for the IDs, or you can get the ID from
> inside the URL clicking the link icon, see screenshot attachment here. I
> don't think you can change the organism ID to something else like a
> readable name unfortunately.
>
> -Colin
>
> On Thu, May 26, 2022 at 12:24 PM Justin Elser <
> jus...@or...> wrote:
>
>> Ok, I think I get it. At least, I think I can get it working but I am a
>> bit confused.
>>
>> So, I noticed in the apollo docker logs that I see this:
>> 2022-05-26 18:10:34,589 [http-nio-8080-exec-4] DEBUG
>> apollo.PreferenceService  - found organism in session
>> org.bbop.apollo.Organism : 34 so returning
>> 2022-05-26 18:10:34,589 [http-nio-8080-exec-4] DEBUG
>> apollo.JbrowseController  - got organism org.bbop.apollo.Organism : 34 for
>> client token 137967108160676781264638533
>> 2022-05-26 18:10:34,649 [http-nio-8080-exec-1] DEBUG
>> apollo.AnnotationEditorController  - handleOperation annotationEditor
>> get_sequence_alterations -> getSequenceAlterations
>> 2022-05-26 18:10:34,650 [http-nio-8080-exec-1] DEBUG
>> apollo.PermissionService  - dataObject does not contain organism (may not
>> be needed)
>> 2022-05-26 18:10:34,652 [http-nio-8080-exec-1] DEBUG
>> apollo.PreferenceService  - found in-memory preference:
>> {"id":96,"organism":{"id":34,"commonName":"Nipponbare","directory":"/data/nipponbare","annotationCount":null,"variantEffectCount":null,"officialGeneSetTrack":null},"currentOrganism":true,"nativeTrackList":true,"sequence":{"id":36,"name":"chr1","organism":{"id":34,"commonName":"Nipponbare","directory":"/data/nipponbare","annotationCount":null,"variantEffectCount":null,"officialGeneSetTrack":null},"length":43270923,"start":0,"end":43270923},"startbp":6587035,"endbp":7241056,"clientToken":"137967108160676781264638533","user":{"id":32,"username":
>> "admin@local.host" <admin@local.host>}}
>>
>> So, it looks like the apollo "id" is 34 for Nipponbare, and similarly 51
>> for ARC.
>>
>> So, I changed the jbrowse.conf to have:
>> [datasets.34]
>> url = ?data=data/nipponbare
>> name = Nipponbare
>> [datasets.51]
>> url = ?data=data/arc
>> name = ARC
>> and data/nipponbare/tracks.conf to have:
>> [general]
>> dataset_id = 34
>>
>> and similar change for data/arc/tracks.conf.
>>
>> Everything works as expected now! I see both Nipponbare and ARC in the
>> "Genome" dropdown, and apollo is showing all data.
>>
>> So, I guess apollo is only using the numeric ID for the dataset instead
>> of using what I tried to set the dataset id? In other words, if I had
>> [datasets.nipponbare] in jbrowse.conf and dataset_id=nipponbare in
>> data/nipponbare/tracks.conf, that is fine for jbrowse, but apollo is only
>> using it's internal ID of 34?
>>
>> I guess I just don't understand why apollo isn't seeing the dataset_id
>> I'm trying to set in jbrowse instead of seeing it's own ID.
>>
>> How can I see what ID apollo is going to use without just checking the
>> logs and seeing what it looks for? Or can I force it somehow to use
>> nipponbare instead of 34?
>>
>> Thanks for the info on JBrowse2/Apollo3, I'll watch for updates.
>>
>> Justin
>>
>> On 5/26/22 11:00 AM, Colin wrote:
>>
>> [This email originated from outside of OSU. Use caution with links and
>> attachments.]
>> The code that is crashing is probably this, seeing renderDatasetSelector
>> in the stack trace
>>
>>
>> https://github.com/GMOD/jbrowse/blob/fd7ebb8a0802db9e09ac34c70689e7a9cfccc615/src/JBrowse/Browser.js#L1214-L1216
>>
>> Since it is crashing there, I think maybe your manually configured
>> datasets are not matching the Apollo configuration of the datasets.
>>
>> If you make them match up, it might fix it, and to do that, you may be
>> able to make the dataset ID be the organism ID that Apollo gives. Would
>> have to update both the datasets and the dataset_id
>>
>> This is where Apollo sets the dataset_id, uses organism ID
>> https://github.com/GMOD/Apollo/blob/1728c280f9a18bd22e07f8b4b9f00a8e24432358/grails-app/controllers/org/bbop/apollo/JbrowseController.groovy#L435-L440
>>
>> To be clear, the dataset ID is what is after the . in the conf format e.g.
>>
>> [datasets.make_this_match_the_organismID]
>> url = ?data=data/nipponbare
>> name = Nipponbare
>>
>>
>> Also, the current generation of Apollo (Apollo 2) does not work with
>> JBrowse 2, but we are working on a new Apollo version that will be
>> integrated with JBrowse 2. It's not ready for use yet but you can keep an
>> eye on https://github.com/GMOD/Apollo3 if interested
>>
>> -Colin
>>
>>
>>
>> On Thu, May 26, 2022 at 9:56 AM Justin Elser <
>> jus...@or...> wrote:
>>
>>> I'm attaching the output from the chrome console. I don't think it's the
>>> non-minified version of the JS though. How would I get that with the docker
>>> version of apollo?
>>>
>>> Also, I've been asked to ask if Apollo works with JBrowse2? Would it be
>>> better to use that instead of JBrowse1?
>>>
>>> Thank you for taking the time to help me.
>>>
>>> Justin
>>>
>>> On 5/25/22 4:51 PM, Colin wrote:
>>>
>>> [This email originated from outside of OSU. Use caution with links and
>>> attachments.]
>>> The logs that are probably most helpful are the "JavaScript console" or
>>> developer console from chrome or firefox e.g.
>>> https://balsamiq.com/support/faqs/browserconsole/
>>>
>>> On Wed, May 25, 2022, 4:33 PM Justin Elser <jus...@or...>
>>> wrote:
>>>
>>>> We may just use Apollo to serve both, but thought I might give it a try
>>>> to see about JBrowse.
>>>>
>>>> I am attaching the output I get when I run the docker container with
>>>> "-e WEBAPOLLO_DEBUG=true".
>>>>
>>>> The blank lines are in between it working and not working. IE, lines
>>>> 1-483 are the initial startup and navigating to the site with Apollo
>>>> working as expected. Lines 487 on are after changing
>>>> data/nipponbare/tracks.conf to have:
>>>> [general]
>>>> dataset_id = nipponbare
>>>>
>>>> I do notice that after the change it is trying to open
>>>> /data/temporary/apollo_data/34-Nipponbare/sample_data/json/volvox/successfully_run
>>>> (line 579) where it isn't before. I don't understand why it would be
>>>> looking for the sample data at all. I never loaded it as a track or
>>>> anything.
>>>>
>>>> I also notice for the initial load where it works that it is
>>>> complaining about the mime_type for .bam files. I did alter the .htaccess
>>>> for the jbrowse but not apollo, so I think those are fixable and unrelated.
>>>> Weirdly enough, the bam track does load fine in Apollo where it didn't in
>>>> JBrowse until I made the change to .htaccess.
>>>>
>>>> If you meant some other logs, please let me know how to get those and I
>>>> will send them to you.
>>>>
>>>> Thanks,
>>>> Justin
>>>>
>>>> On 5/25/22 2:18 PM, Colin wrote:
>>>>
>>>> [This email originated from outside of OSU. Use caution with links and
>>>> attachments.]
>>>> One option is to use Apollo to serve your jbrowse instances, Apollo can
>>>> serve public jbrowse instances so you may not need to configure jbrowse
>>>> separately
>>>>
>>>>
>>>> If you do want it separate, then we would probably need to debug that
>>>> error. If you have the stack trace from the developer console, it might
>>>> narrow down exactly where the error comes from. If the stack trace is
>>>> minified and hard to read, can possibly use a "dev" version of jbrowse if
>>>> it is too unreadable since it does not minify the builds!
>>>>
>>>>
>>>>
>>>> -Colin
>>>>
>>>> On Wed, May 25, 2022 at 1:03 PM Justin Elser <
>>>> jus...@or...> wrote:
>>>>
>>>>> Yeah, so I guess the problem is that if I don't add the "dataset_id"
>>>>> to each data/(species)/tracks.conf file, apollo works fine, but then I
>>>>> can't get the dataset selector in jbrowse. As I have it right now, Apollo
>>>>> is fine, but I have no way to switch to a different dataset in JBrowse.
>>>>>
>>>>>
>>>>> I was messing around with jbrowse.conf, data/tracks.conf, and
>>>>> data/(species)/tracks.conf, and was able to get a list of the species under
>>>>> the "Genome" tab. But if I don't have anything in
>>>>> data/(species)/tracks.conf, I don't. However, if I do add it like in the
>>>>> documentation, the species are listed under there:
>>>>>
>>>>> But then, apollo breaks:
>>>>>
>>>>>
>>>>> So, I guess I need to get the dataset_selector working in JBrowse,
>>>>> while not breaking Apollo.
>>>>>
>>>>> I hope that clears it up more.
>>>>>
>>>>> Thanks,
>>>>> Justin
>>>>>
>>>>> On 5/25/22 11:50 AM, Colin wrote:
>>>>>
>>>>> [This email originated from outside of OSU. Use caution with links and
>>>>> attachments.]
>>>>> I haven't evaluated the whole post here, but note that Apollo
>>>>> automatically creates a dataset selector from assemblies that you configure
>>>>> through that Apollo interface
>>>>>
>>>>>
>>>>> -Colin
>>>>>
>>>>> On Wed, May 25, 2022 at 12:21 PM Justin Elser <
>>>>> jus...@or...> wrote:
>>>>>
>>>>>> Hi all,
>>>>>>
>>>>>> I have set up a jbrowse 1.16.11 instance (sorry, not publicly
>>>>>> available)
>>>>>> and added 2 species (well, different cultivars) by doing the
>>>>>> following:
>>>>>> bin/prepare-refseqs.pl --out data/nipponbare --fasta
>>>>>> source_files/RAPDB-Reference-Nipponbare_chr_fixed.fasta
>>>>>> bin/flatfile-to-json.pl --out data/nipponbare --trackType
>>>>>> CanvasFeatures
>>>>>> --trackLabel MSU7.0 -gff source_files/MSU7.0.gff3
>>>>>> bin/generate-names.pl --out data/nipponbare
>>>>>>
>>>>>> bin/prepare-refseqs.pl --out data/arc --fasta
>>>>>> source_files/magic_16/oryza_sativa_arc.fa
>>>>>> bin/flatfile-to-json.pl --out data/arc --trackType CanvasFeatures
>>>>>> --trackLabel Genes -gff source_files/magic_16/oryza_sativa_arc.gff
>>>>>> bin/generate-names.pl --out data/arc
>>>>>>
>>>>>> Then I edited the jbrowse.conf file as explained in
>>>>>> https://jbrowse.org/docs/dataset_selector.html to have:
>>>>>> dataRoot = data/nipponbare
>>>>>> [datasets.nipponbare]
>>>>>> url = ?data=data/nipponbare
>>>>>> name = Nipponbare
>>>>>> [datasets.arc]
>>>>>> url = ?data=data/arc
>>>>>> name = ARC
>>>>>>
>>>>>> And all seems to work fine, except that I don't see the dropdown to
>>>>>> switch datasets, so I can't actually see the ARC dataset. Although I
>>>>>> have by messing around with jbrowse.conf and tracks.conf gotten it to
>>>>>> work, but at this point I've left it out.
>>>>>>
>>>>>> However, the issue I'm having is actually with Apollo. I have the
>>>>>> docker
>>>>>> instance of apollo running and it seems to be fine as configured in a
>>>>>> systemd unit file:
>>>>>> ExecStart=/usr/bin/docker run --rm --name %n \
>>>>>>          -e APOLLO_PATH=apollo \
>>>>>>          -v /data/www/panoryza/jbrowse/data:/data \
>>>>>>          -v /data/www/panoryza/apollo/postgres:/var/lib/postgresql \
>>>>>>          -v
>>>>>> /data/www/panoryza/apollo/apollo_data:/data/temporary/apollo_data \
>>>>>>          -p 8887:8080 \
>>>>>>          gmod/apollo:latest
>>>>>>
>>>>>> Adding Nipponbare as an organism with "Directory" /data/nipponbare
>>>>>> works
>>>>>> fine and I can see the tracks I've added.
>>>>>>
>>>>>> Now, here is where the issue I have starts. If I edit the
>>>>>> data/nipponbare/tracks.conf file as shown in the dataset selector
>>>>>> documentation above:
>>>>>> [general]
>>>>>> dataset_id = nipponbare
>>>>>>
>>>>>> Apollo then shows the following error:
>>>>>> Error message(s):
>>>>>>      TypeError: Cannot read properties of undefined (reading 'name').
>>>>>>
>>>>>> Clearing out the data/nipponbare/tracks.conf file allows apollo to
>>>>>> work.
>>>>>> Now, the error only appears in apollo, jbrowse works fine with the
>>>>>> edits.
>>>>>>
>>>>>> I'm a bit confused about how this should be configured to work. I
>>>>>> actually have 14 more "species" to add, but waiting till I at least
>>>>>> get
>>>>>> it working with one. The documentation isn't clear to me on the
>>>>>> difference between adding the datasets to jbrowse.conf vs
>>>>>> data/tracks.conf vs data/(species)/tracks.conf.
>>>>>>
>>>>>> Please let me know if you need any more information.
>>>>>>
>>>>>> Thanks,
>>>>>> Justin
>>>>>>
>>>>>> --
>>>>>> **********************************************************
>>>>>> *                                                        *
>>>>>> *  Justin Elser                                          *
>>>>>> *  Computational Biology Research Associate              *
>>>>>> *  Dept. of Botany and Plant Pathology                   *
>>>>>> *  Jaiswal Lab                                           *
>>>>>> *  Oregon State University                               *
>>>>>> *                                                        *
>>>>>> *  email: jus...@or...                   *
>>>>>> *                                                        *
>>>>>> **********************************************************
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Gmod-ajax mailing list
>>>>>> Gmo...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>>>
>>>>>
>>>>> --
>>>>> **********************************************************
>>>>> *                                                        *
>>>>> *  Justin Elser                                          *
>>>>> *  Computational Biology Research Associate              *
>>>>> *  Dept. of Botany and Plant Pathology                   *
>>>>> *  Jaiswal Lab                                           *
>>>>> *  Oregon State University                               *
>>>>> *                                                        *
>>>>> *  email: jus...@or...                   *
>>>>> *                                                        *
>>>>> **********************************************************
>>>>>
>>>>>
>>>> --
>>>> **********************************************************
>>>> *                                                        *
>>>> *  Justin Elser                                          *
>>>> *  Computational Biology Research Associate              *
>>>> *  Dept. of Botany and Plant Pathology                   *
>>>> *  Jaiswal Lab                                           *
>>>> *  Oregon State University                               *
>>>> *                                                        *
>>>> *  email: jus...@or...                   *
>>>> *                                                        *
>>>> **********************************************************
>>>>
>>>>
>>> --
>>> **********************************************************
>>> *                                                        *
>>> *  Justin Elser                                          *
>>> *  Computational Biology Research Associate              *
>>> *  Dept. of Botany and Plant Pathology                   *
>>> *  Jaiswal Lab                                           *
>>> *  Oregon State University                               *
>>> *                                                        *
>>> *  email: jus...@or...                   *
>>> *                                                        *
>>> **********************************************************
>>>
>>>
>> --
>> **********************************************************
>> *                                                        *
>> *  Justin Elser                                          *
>> *  Computational Biology Research Associate              *
>> *  Dept. of Botany and Plant Pathology                   *
>> *  Jaiswal Lab                                           *
>> *  Oregon State University                               *
>> *                                                        *
>> *  email: jus...@or...                   *
>> *                                                        *
>> **********************************************************
>>
>>
> --
> **********************************************************
> *                                                        *
> *  Justin Elser                                          *
> *  Computational Biology Research Associate              *
> *  Dept. of Botany and Plant Pathology                   *
> *  Jaiswal Lab                                           *
> *  Oregon State University                               *
> *                                                        *
> *  email: jus...@or...                   *
> *                                                        *
> **********************************************************
>
>

Re: [Gmod-ajax] JBrowse XML parsing errors

[Colin <col...@gm...>]

Hi Vaneet,

This console log message is just a browser specific thing with Firefox, but
as far as I know does not indicate anything is wrong. It is just something
Firefox says when a .conf file is downloaded, but the .conf file is
otherwise interpreted fine by the JBrowse code itself. I think you can
ignore the message


-Colin

On Wed, Jun 1, 2022 at 11:59 AM Vaneet Lotay <van...@uc...>
wrote:

> Hi,
>
> I attached a screenshot of the XML parsing errors from the console of my
> Firefox browser, which I'm a little confused about.  I checked the actual
> configuration files that these errors denote, and I don't see anything
> wrong or any hidden characters that are there on the first line.  I don't
> think these are file specific though as no matter what genome I switch to
> in JBrowse I see the same errors, that is those genomes for which I have an
> extra configuration file for functions that's named 'functions.conf'.  The
> jbrowse.conf error always appears.  I don't see any visible problem on the
> browser tracks that results from these errors but I just want to eliminate
> them to make sure.
>
> After looking at the JBrowse 1 troubleshooting page, I took the suggestion
> to install the libexpat1-dev package and then rerun the setup.sh script,
> but errors are still there on Firefox.  If I load the page in Microsoft
> Edge browser, I don't see the errors there, so I'm wondering if it's
> browser specific? Is anyone aware of any fixes for this specific issue?
>
> Thanks,
>
> Vaneet
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] Dataset selector in apollo

[Justin E. <jus...@or...>]

<html><head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
  </head>
  <body>
    So, this is hopefully an easy question, and I may have just missed
    it in the documentation, but is there a way to change the order in
    which the datasets show up in the genome selector?<br>
    <br>
    It looks like they get added in the order in which they were added,
    or possibly alphanumeric by dataset_id?<br>
    <br>
    In the below screenshot, I'd like Minghui63 to be between Liu Xu and
    Nagina 22, but since it is the last one I added, it shows up last. I
    have it where I want it in the jbrowse.conf file, but it still shows
    up last. I don't totally want them in alphabetical order, as I would
    like Nipponbare to be first.<br>
    <img src="cid:par...@or..." alt="" width="926" height="559"><br>
    Is it possible to change this?<br>
    <br>
    Thanks,<br>
    Justin<br>
    <br>
    <div class="moz-cite-prefix">On 5/26/22 2:05 PM, Colin wrote:<br>
    </div>
    <blockquote type="cite" cite="mid:CA+ZENaJDHxrgizJpUHoBND2OKstw3p957qjzJtBUnCU=WNPT=g...@ma...">
      
      <p><span style="color:#D73F09;">[This email originated from
          outside of OSU. Use caution with links and attachments.]</span></p>
      <div>
        <div dir="ltr">&gt;Everything works as expected now! I see both
          Nipponbare and ARC in the &quot;Genome&quot; dropdown, and apollo is
          showing all data.<br>
          <div><br>
          </div>
          <div>Excellent:)</div>
          <div><br>
          </div>
          <div>&gt;So, I guess apollo is only using the numeric ID for
            the dataset instead of using what I tried to set the dataset
            id? In other words, if I had [datasets.nipponbare] in
            jbrowse.conf and dataset_id=nipponbare in
            data/nipponbare/tracks.conf, that is fine for jbrowse, but
            apollo is only using it's internal ID of 34?</div>
          <div><br>
          </div>
          <div>You can inspect the database for the IDs, or you can get
            the ID from inside the URL clicking the link icon, see
            screenshot attachment here. I don't think you can change the
            organism ID to something else like a readable name
            unfortunately.</div>
          <div><br>
          </div>
          <div>-Colin</div>
        </div>
        <br>
        <div class="gmail_quote">
          <div dir="ltr" class="gmail_attr">On Thu, May 26, 2022 at
            12:24 PM Justin Elser &lt;<a href="mailto:jus...@or..." moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>&gt;
            wrote:<br>
          </div>
          <blockquote class="gmail_quote" style="margin:0px 0px 0px
            0.8ex;border-left:1px solid
            rgb(204,204,204);padding-left:1ex">
            <div>Ok, I think I get it. At least, I think I can get it
              working but I am a bit confused.<br>
              <br>
              So, I noticed in the apollo docker logs that I see this:<br>
              2022-05-26 18:10:34,589 [http-nio-8080-exec-4] DEBUG
              apollo.PreferenceService&nbsp; - found organism in session
              org.bbop.apollo.Organism : 34 so returning<br>
              2022-05-26 18:10:34,589 [http-nio-8080-exec-4] DEBUG
              apollo.JbrowseController&nbsp; - got organism
              org.bbop.apollo.Organism : 34 for client token
              137967108160676781264638533<br>
              2022-05-26 18:10:34,649 [http-nio-8080-exec-1] DEBUG
              apollo.AnnotationEditorController&nbsp; - handleOperation
              annotationEditor get_sequence_alterations -&gt;
              getSequenceAlterations<br>
              2022-05-26 18:10:34,650 [http-nio-8080-exec-1] DEBUG
              apollo.PermissionService&nbsp; - dataObject does not contain
              organism (may not be needed)<br>
              2022-05-26 18:10:34,652 [http-nio-8080-exec-1] DEBUG
              apollo.PreferenceService&nbsp; - found in-memory preference:
{&quot;id&quot;:96,&quot;organism&quot;:{&quot;id&quot;:34,&quot;commonName&quot;:&quot;Nipponbare&quot;,&quot;directory&quot;:&quot;/data/nipponbare&quot;,&quot;annotationCount&quot;:null,&quot;variantEffectCount&quot;:null,&quot;officialGeneSetTrack&quot;:null},&quot;currentOrganism&quot;:true,&quot;nativeTrackList&quot;:true,&quot;sequence&quot;:{&quot;id&quot;:36,&quot;name&quot;:&quot;chr1&quot;,&quot;organism&quot;:{&quot;id&quot;:34,&quot;commonName&quot;:&quot;Nipponbare&quot;,&quot;directory&quot;:&quot;/data/nipponbare&quot;,&quot;annotationCount&quot;:null,&quot;variantEffectCount&quot;:null,&quot;officialGeneSetTrack&quot;:null},&quot;length&quot;:43270923,&quot;start&quot;:0,&quot;end&quot;:43270923},&quot;startbp&quot;:6587035,&quot;endbp&quot;:7241056,&quot;clientToken&quot;:&quot;137967108160676781264638533&quot;,&quot;user&quot;:{&quot;id&quot;:32,&quot;username&quot;:<a href="mailto:admin@local.host" target="_blank" moz-do-not-send="true">&quot;admin@local.host&quot;</a>}}<br>
              <br>
              So, it looks like the apollo &quot;id&quot; is 34 for Nipponbare,
              and similarly 51 for ARC.<br>
              <br>
              So, I changed the jbrowse.conf to have:<br>
              [datasets.34]<br>
              url = ?data=data/nipponbare<br>
              name = Nipponbare<br>
              [datasets.51]<br>
              url = ?data=data/arc<br>
              name = ARC<br>
              and data/nipponbare/tracks.conf to have:<br>
              [general]<br>
              dataset_id = 34<br>
              <br>
              and similar change for data/arc/tracks.conf.<br>
              <br>
              Everything works as expected now! I see both Nipponbare
              and ARC in the &quot;Genome&quot; dropdown, and apollo is showing
              all data.<br>
              <br>
              So, I guess apollo is only using the numeric ID for the
              dataset instead of using what I tried to set the dataset
              id? In other words, if I had [datasets.nipponbare] in
              jbrowse.conf and dataset_id=nipponbare in
              data/nipponbare/tracks.conf, that is fine for jbrowse, but
              apollo is only using it's internal ID of 34?<br>
              <br>
              I guess I just don't understand why apollo isn't seeing
              the dataset_id I'm trying to set in jbrowse instead of
              seeing it's own ID.<br>
              <br>
              How can I see what ID apollo is going to use without just
              checking the logs and seeing what it looks for? Or can I
              force it somehow to use nipponbare instead of 34?<br>
              <br>
              Thanks for the info on JBrowse2/Apollo3, I'll watch for
              updates.<br>
              <br>
              Justin<br>
              <br>
              <div>On 5/26/22 11:00 AM, Colin wrote:<br>
              </div>
              <blockquote type="cite">
                <p><span style="color:rgb(215,63,9)">[This email
                    originated from outside of OSU. Use caution with
                    links and attachments.]</span></p>
                <div>
                  <div dir="ltr">
                    <div>The code that is crashing is probably this,
                      seeing renderDatasetSelector in the stack trace</div>
                    <div><br>
                    </div>
                    <div><a href="https://github.com/GMOD/jbrowse/blob/fd7ebb8a0802db9e09ac34c70689e7a9cfccc615/src/JBrowse/Browser.js#L1214-L1216" originalsrc="https://github.com/GMOD/jbrowse/blob/fd7ebb8a0802db9e09ac34c70689e7a9cfccc615/src/JBrowse/Browser.js#L1214-L1216" shash="uhjL/hW/sjvOdWW3sAmi7MXxNww/o/kUrVgnDjMwc8zMNV4To9B20gCN/oqOaByxVsHC7IkHHs85yF8qz4KWCNInA+Rxto66yUepLZLhE8P0JFq7MctzCPRJB2nLP2wk+i73yQ5ndWO5T521RXLUlT4E0vLE7Jg+6aoDt3SU4eM=" title="Unmangled Microsoft Safelink" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">https://github.com/GMOD/jbrowse/blob/fd7ebb8a0802db9e09ac34c70689e7a9cfccc615/src/JBrowse/Browser.js#L1214-L1216</a><br>
                    </div>
                    <div><br>
                    </div>
                    Since it is crashing there, I think maybe your
                    manually configured datasets&nbsp;are not matching the
                    Apollo configuration of the datasets.
                    <div><br>
                    </div>
                    <div>If you make them match up, it might fix it, and
                      to do that, you may be able to make the dataset ID
                      be the organism ID that Apollo gives. Would have
                      to update both the datasets and the dataset_id</div>
                    <div><br>
                    </div>
                    <div>This is where Apollo sets the dataset_id, uses
                      organism ID&nbsp;<a href="https://github.com/GMOD/Apollo/blob/1728c280f9a18bd22e07f8b4b9f00a8e24432358/grails-app/controllers/org/bbop/apollo/JbrowseController.groovy#L435-L440" originalsrc="https://github.com/GMOD/Apollo/blob/1728c280f9a18bd22e07f8b4b9f00a8e24432358/grails-app/controllers/org/bbop/apollo/JbrowseController.groovy#L435-L440" shash="jEuwZ0dqegE2z/ek9p2MUYGduI48cfLvBnD+jGpjdItqWKipFg2K5lWfJlacMpQmxUbzuFh1Af2wNKtyYJC01X00kZqfyZCWKPE+AeksUcAS+e1NiEzQvjkT+MBtFW/2MJwV6N5wdBW0/g1FKDERvaIEXSmv/LPeKxeeA0U4Qmo=" title="Unmangled Microsoft Safelink" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">https://github.com/GMOD/Apollo/blob/1728c280f9a18bd22e07f8b4b9f00a8e24432358/grails-app/controllers/org/bbop/apollo/JbrowseController.groovy#L435-L440</a><br>
                      <div><br>
                      </div>
                      <div>To be clear, the dataset ID is what is after
                        the . in the conf format e.g.</div>
                      <div><br>
                      </div>
                      <div>[datasets.make_this_match_the_organismID]<br>
                        url = ?data=data/nipponbare<br>
                        name = Nipponbare<br>
                      </div>
                      <div><br>
                      </div>
                      <div><br>
                      </div>
                      <div>Also, the current generation of Apollo
                        (Apollo 2) does not work with JBrowse 2, but we
                        are working on a new Apollo version that will be
                        integrated with JBrowse 2. It's not ready for
                        use yet but you can keep an eye on&nbsp;<a href="https://github.com/GMOD/Apollo3" originalsrc="https://github.com/GMOD/Apollo3" shash="ijgN7D+gf4dZ7q0XGy4q02i8BxgPVkel68Ek2TCid0GhO7rem4wYpbfPl7KlLrcrxutD/d8x+jAbIcTYnzSVrlIsow+sbW+aPZoQS4yt7O+bZo/82PzDTbQ8AW1182d9ViNSXVhYu6LHZhSrLC32vNc/GVgpkatSQBe7zIbwWAs=" title="Unmangled Microsoft Safelink" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">https://github.com/GMOD/Apollo3</a>
                        if interested</div>
                      <div><br>
                      </div>
                      <div>-Colin</div>
                      <div><br>
                      </div>
                      <div><br>
                      </div>
                    </div>
                  </div>
                  <br>
                  <div class="gmail_quote">
                    <div dir="ltr" class="gmail_attr">On Thu, May 26,
                      2022 at 9:56 AM Justin Elser &lt;<a href="mailto:jus...@or..." target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>&gt;
                      wrote:<br>
                    </div>
                    <blockquote class="gmail_quote" style="margin:0px
                      0px 0px 0.8ex;border-left:1px solid
                      rgb(204,204,204);padding-left:1ex">
                      <div>I'm attaching the output from the chrome
                        console. I don't think it's the non-minified
                        version of the JS though. How would I get that
                        with the docker version of apollo?<br>
                        <br>
                        Also, I've been asked to ask if Apollo works
                        with JBrowse2? Would it be better to use that
                        instead of JBrowse1?<br>
                        <br>
                        Thank you for taking the time to help me.<br>
                        <br>
                        Justin<br>
                        <br>
                        <div>On 5/25/22 4:51 PM, Colin wrote:<br>
                        </div>
                        <blockquote type="cite">
                          <p><span style="color:rgb(215,63,9)">[This
                              email originated from outside of OSU. Use
                              caution with links and attachments.]</span></p>
                          <div>
                            <div dir="auto">The logs that are probably
                              most helpful are the &quot;JavaScript console&quot;
                              or developer console from chrome or
                              firefox e.g.
                              <a href="https://balsamiq.com/support/faqs/browserconsole/" originalsrc="https://balsamiq.com/support/faqs/browserconsole/" shash="mQLrKBEXj/KgA6uhAKsooEZXtW49iY/ID1YcURrcIx/erCmYD7Iz4TQ6WrIwcDeS3zSUHzMlJStSEm4pSoK0FQdoamnwLbBEEKYWXC45gFMgyQJfJHl32sVU+9fTJ0VPoOdWsSejvG1eyvvVRhI9s4TqrlkU7KHDDNuNQT9iSLA=" rel="noreferrer" title="Unmangled
                                Microsoft Safelink" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">
https://balsamiq.com/support/faqs/browserconsole/</a></div>
                            <br>
                            <div class="gmail_quote">
                              <div dir="ltr" class="gmail_attr">On Wed,
                                May 25, 2022, 4:33 PM Justin Elser &lt;<a href="mailto:jus...@or..." rel="noreferrer noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>&gt;
                                wrote:<br>
                              </div>
                              <blockquote class="gmail_quote" style="margin:0px 0px 0px
                                0.8ex;border-left:1px solid
                                rgb(204,204,204);padding-left:1ex">
                                <div>We may just use Apollo to serve
                                  both, but thought I might give it a
                                  try to see about JBrowse.<br>
                                  <br>
                                  I am attaching the output I get when I
                                  run the docker container with &quot;-e
                                  WEBAPOLLO_DEBUG=true&quot;.<br>
                                  <br>
                                  The blank lines are in between it
                                  working and not working. IE, lines
                                  1-483 are the initial startup and
                                  navigating to the site with Apollo
                                  working as expected. Lines 487 on are
                                  after changing
                                  data/nipponbare/tracks.conf to have:<br>
                                  [general]<br>
                                  dataset_id = nipponbare<br>
                                  <br>
                                  I do notice that after the change it
                                  is trying to open
/data/temporary/apollo_data/34-Nipponbare/sample_data/json/volvox/successfully_run
                                  (line 579) where it isn't before. I
                                  don't understand why it would be
                                  looking for the sample data at all. I
                                  never loaded it as a track or
                                  anything.<br>
                                  <br>
                                  I also notice for the initial load
                                  where it works that it is complaining
                                  about the mime_type for .bam files. I
                                  did alter the .htaccess for the
                                  jbrowse but not apollo, so I think
                                  those are fixable and unrelated.
                                  Weirdly enough, the bam track does
                                  load fine in Apollo where it didn't in
                                  JBrowse until I made the change to
                                  .htaccess.<br>
                                  <br>
                                  If you meant some other logs, please
                                  let me know how to get those and I
                                  will send them to you.<br>
                                  <br>
                                  Thanks,<br>
                                  Justin<br>
                                  <br>
                                  <div>On 5/25/22 2:18 PM, Colin wrote:<br>
                                  </div>
                                  <blockquote type="cite">
                                    <p><span style="color:rgb(215,63,9)">[This
                                        email originated from outside of
                                        OSU. Use caution with links and
                                        attachments.]</span></p>
                                    <div>
                                      <div dir="ltr">One option is to
                                        use Apollo to serve your jbrowse
                                        instances, Apollo can serve
                                        public jbrowse instances so you
                                        may not need to configure
                                        jbrowse separately
                                        <div><br>
                                        </div>
                                        <div><br>
                                          <div>If you do want it
                                            separate, then we would
                                            probably need to debug that
                                            error. If you have the stack
                                            trace from the developer
                                            console, it might narrow
                                            down exactly where the error
                                            comes from. If the stack
                                            trace is minified and hard
                                            to read, can possibly use a
                                            &quot;dev&quot; version of jbrowse if
                                            it is too unreadable since
                                            it does not minify the
                                            builds!
                                            <div><br>
                                            </div>
                                            <div><br>
                                            </div>
                                            <div><br>
                                            </div>
                                            <div>-Colin</div>
                                          </div>
                                        </div>
                                      </div>
                                      <br>
                                      <div class="gmail_quote">
                                        <div dir="ltr" class="gmail_attr">On Wed, May
                                          25, 2022 at 1:03 PM Justin
                                          Elser &lt;<a href="mailto:jus...@or..." rel="noreferrer noreferrer
                                            noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>&gt;
                                          wrote:<br>
                                        </div>
                                        <blockquote class="gmail_quote" style="margin:0px 0px 0px
                                          0.8ex;border-left:1px solid
                                          rgb(204,204,204);padding-left:1ex">
                                          <div>Yeah, so I guess the
                                            problem is that if I don't
                                            add the &quot;dataset_id&quot; to each
                                            data/(species)/tracks.conf
                                            file, apollo works fine, but
                                            then I can't get the dataset
                                            selector in jbrowse. As I
                                            have it right now, Apollo is
                                            fine, but I have no way to
                                            switch to a different
                                            dataset in JBrowse.<br>
                                            <img alt="" moz-do-not-send="true" width="1073" height="648"><br>
                                            <br>
                                            I was messing around with
                                            jbrowse.conf,
                                            data/tracks.conf, and
                                            data/(species)/tracks.conf,
                                            and was able to get a list
                                            of the species under the
                                            &quot;Genome&quot; tab. But if I don't
                                            have anything in
                                            data/(species)/tracks.conf,
                                            I don't. However, if I do
                                            add it like in the
                                            documentation, the species
                                            are listed under there:<br>
                                            <img alt="" moz-do-not-send="true" width="1021" height="616"><br>
                                            But then, apollo breaks:<br>
                                            <img alt="" moz-do-not-send="true" width="972" height="587"><br>
                                            <br>
                                            So, I guess I need to get
                                            the dataset_selector working
                                            in JBrowse, while not
                                            breaking Apollo.<br>
                                            <br>
                                            I hope that clears it up
                                            more.<br>
                                            <br>
                                            Thanks,<br>
                                            Justin<br>
                                            <br>
                                            <div>On 5/25/22 11:50 AM,
                                              Colin wrote:<br>
                                            </div>
                                            <blockquote type="cite">
                                              <p><span style="color:rgb(215,63,9)">[This
                                                  email originated from
                                                  outside of OSU. Use
                                                  caution with links and
                                                  attachments.]</span></p>
                                              <div>
                                                <div dir="ltr">
                                                  <div>I haven't
                                                    evaluated the whole
                                                    post here, but note
                                                    that Apollo
                                                    automatically
                                                    creates a dataset
                                                    selector from
                                                    assemblies that you
                                                    configure through
                                                    that Apollo
                                                    interface</div>
                                                  <div><br>
                                                  </div>
                                                  <div>
                                                    <div><br>
                                                    </div>
                                                    <div>-Colin</div>
                                                  </div>
                                                </div>
                                                <br>
                                                <div class="gmail_quote">
                                                  <div dir="ltr" class="gmail_attr">On
                                                    Wed, May 25, 2022 at
                                                    12:21 PM Justin
                                                    Elser &lt;<a href="mailto:jus...@or..." rel="noreferrer
                                                      noreferrer
                                                      noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>&gt;
                                                    wrote:<br>
                                                  </div>
                                                  <blockquote class="gmail_quote" style="margin:0px
                                                    0px 0px
                                                    0.8ex;border-left:1px
                                                    solid
                                                    rgb(204,204,204);padding-left:1ex">
                                                    Hi all,<br>
                                                    <br>
                                                    I have set up a
                                                    jbrowse 1.16.11
                                                    instance (sorry, not
                                                    publicly available)
                                                    <br>
                                                    and added 2 species
                                                    (well, different
                                                    cultivars) by doing
                                                    the following:<br>
                                                    bin/<a href="http://prepare-refseqs.pl/" originalsrc="http://prepare-refseqs.pl/" shash="B+jVefrKrefTFTkcGlf7AYg0BmqVa9mHbZ5u3RmfVgw9EgDXdiCkXHCajEI4Lygb7aSj1PpKYphvQ/USOKWeUhSfD2nT5VWZGPVTF5P0+y/xPpBU1sLkOBmfsGK2+TaAmrT+UQga0p/nP35BW8Mq1dalvC2r3lUs3/UleGwiOqQ=" rel="noreferrer
                                                      noreferrer
                                                      noreferrer
                                                      noreferrer" title="Unmangled
                                                      Microsoft
                                                      Safelink" target="_blank" moz-do-not-send="true">prepare-refseqs.pl</a>
                                                    --out
                                                    data/nipponbare
                                                    --fasta <br>
source_files/RAPDB-Reference-Nipponbare_chr_fixed.fasta<br>
                                                    bin/<a href="http://flatfile-to-json.pl/" originalsrc="http://flatfile-to-json.pl/" shash="fjBFMWnFVufXG8eIOm1XK0A0/yYJeqzTnS0Ql/D7wnwq0G7B+0+GOV1/Sb8InKJYF/xc2dFWDlrw2JN/uaOS1dGpnYKCDMYCKQu2E6h3IgFxUSdaPBVlaxssN5AcH412URCrcKYI7bpmvrS6HIgus5UMnBeLjRzI+gHaolCZeF4=" rel="noreferrer
                                                      noreferrer
                                                      noreferrer
                                                      noreferrer" title="Unmangled
                                                      Microsoft
                                                      Safelink" target="_blank" moz-do-not-send="true">flatfile-to-json.pl</a>
                                                    --out
                                                    data/nipponbare
                                                    --trackType
                                                    CanvasFeatures <br>
                                                    --trackLabel MSU7.0
                                                    -gff
                                                    source_files/MSU7.0.gff3<br>
                                                    bin/<a href="http://generate-names.pl/" originalsrc="http://generate-names.pl/" shash="zRCP36TRaHjgLXG5Apd+kvq2QhCT1B4RxEqXILumVcU00nPEo1edu3Lx4Xwc0zzDoQFai54UqYndjmOjL8BpgihHC+u79yKV3Ue5xG0i5LDQdAXIPaPZNICqsYwQHCpj5B/s7KqzwiH6NIUJAyNpgbZ+0/zCR/8PiHN5lEWdy/A=" rel="noreferrer
                                                      noreferrer
                                                      noreferrer
                                                      noreferrer" title="Unmangled
                                                      Microsoft
                                                      Safelink" target="_blank" moz-do-not-send="true">generate-names.pl</a>
                                                    --out
                                                    data/nipponbare<br>
                                                    <br>
                                                    bin/<a href="http://prepare-refseqs.pl/" originalsrc="http://prepare-refseqs.pl/" shash="B+jVefrKrefTFTkcGlf7AYg0BmqVa9mHbZ5u3RmfVgw9EgDXdiCkXHCajEI4Lygb7aSj1PpKYphvQ/USOKWeUhSfD2nT5VWZGPVTF5P0+y/xPpBU1sLkOBmfsGK2+TaAmrT+UQga0p/nP35BW8Mq1dalvC2r3lUs3/UleGwiOqQ=" rel="noreferrer
                                                      noreferrer
                                                      noreferrer
                                                      noreferrer" title="Unmangled
                                                      Microsoft
                                                      Safelink" target="_blank" moz-do-not-send="true">prepare-refseqs.pl</a>
                                                    --out data/arc
                                                    --fasta <br>
source_files/magic_16/oryza_sativa_arc.fa<br>
                                                    bin/<a href="http://flatfile-to-json.pl/" originalsrc="http://flatfile-to-json.pl/" shash="fjBFMWnFVufXG8eIOm1XK0A0/yYJeqzTnS0Ql/D7wnwq0G7B+0+GOV1/Sb8InKJYF/xc2dFWDlrw2JN/uaOS1dGpnYKCDMYCKQu2E6h3IgFxUSdaPBVlaxssN5AcH412URCrcKYI7bpmvrS6HIgus5UMnBeLjRzI+gHaolCZeF4=" rel="noreferrer
                                                      noreferrer
                                                      noreferrer
                                                      noreferrer" title="Unmangled
                                                      Microsoft
                                                      Safelink" target="_blank" moz-do-not-send="true">flatfile-to-json.pl</a>
                                                    --out data/arc
                                                    --trackType
                                                    CanvasFeatures <br>
                                                    --trackLabel Genes
                                                    -gff
                                                    source_files/magic_16/oryza_sativa_arc.gff<br>
                                                    bin/<a href="http://generate-names.pl/" originalsrc="http://generate-names.pl/" shash="zRCP36TRaHjgLXG5Apd+kvq2QhCT1B4RxEqXILumVcU00nPEo1edu3Lx4Xwc0zzDoQFai54UqYndjmOjL8BpgihHC+u79yKV3Ue5xG0i5LDQdAXIPaPZNICqsYwQHCpj5B/s7KqzwiH6NIUJAyNpgbZ+0/zCR/8PiHN5lEWdy/A=" rel="noreferrer
                                                      noreferrer
                                                      noreferrer
                                                      noreferrer" title="Unmangled
                                                      Microsoft
                                                      Safelink" target="_blank" moz-do-not-send="true">generate-names.pl</a>
                                                    --out data/arc<br>
                                                    <br>
                                                    Then I edited the
                                                    jbrowse.conf file as
                                                    explained in <br>
                                                    <a href="https://jbrowse.org/docs/dataset_selector.html" originalsrc="https://jbrowse.org/docs/dataset_selector.html" shash="jY79EUL0uW/+K/a6fNnZys8zoiMKyO9tOE4x4BQUcOQm3vxV9gHr/0WYyaQ2I4DhVgua0HTeyR3v6ZBLcVje2jAKG4ny/C2AGUFBmjmAAOjMSvk6XMlH4yglI+9YKOnbsV46xyWJJ+3WbG43nZ6gspE/4txV0LGcHFUJNUfyF80=" rel="noreferrer
                                                      noreferrer
                                                      noreferrer
                                                      noreferrer" title="Unmangled
                                                      Microsoft
                                                      Safelink" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">https://jbrowse.org/docs/dataset_selector.html</a>
                                                    to have:<br>
                                                    dataRoot =
                                                    data/nipponbare<br>
[datasets.nipponbare]<br>
                                                    url =
                                                    ?data=data/nipponbare<br>
                                                    name = Nipponbare<br>
                                                    [datasets.arc]<br>
                                                    url = ?data=data/arc<br>
                                                    name = ARC<br>
                                                    <br>
                                                    And all seems to
                                                    work fine, except
                                                    that I don't see the
                                                    dropdown to <br>
                                                    switch datasets, so
                                                    I can't actually see
                                                    the ARC dataset.
                                                    Although I <br>
                                                    have by messing
                                                    around with
                                                    jbrowse.conf and
                                                    tracks.conf gotten
                                                    it to <br>
                                                    work, but at this
                                                    point I've left it
                                                    out.<br>
                                                    <br>
                                                    However, the issue
                                                    I'm having is
                                                    actually with
                                                    Apollo. I have the
                                                    docker <br>
                                                    instance of apollo
                                                    running and it seems
                                                    to be fine as
                                                    configured in a <br>
                                                    systemd unit file:<br>
ExecStart=/usr/bin/docker run --rm --name %n \<br>
                                                    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -e
                                                    APOLLO_PATH=apollo \<br>
                                                    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -v
                                                    /data/www/panoryza/jbrowse/<a rel="noreferrer
                                                      noreferrer
                                                      noreferrer" moz-do-not-send="true">data:/data</a>
                                                    \<br>
                                                    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -v
                                                    /data/www/panoryza/apollo/postgres:/var/lib/postgresql
                                                    \<br>
                                                    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -v <br>
/data/www/panoryza/apollo/apollo_<a rel="noreferrer noreferrer
                                                      noreferrer" moz-do-not-send="true">data:/data/temporary/apollo_data</a>
                                                    \<br>
                                                    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -p
                                                    8887:8080 \<br>
                                                    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
                                                    gmod/apollo:latest<br>
                                                    <br>
                                                    Adding Nipponbare as
                                                    an organism with
                                                    &quot;Directory&quot;
                                                    /data/nipponbare
                                                    works <br>
                                                    fine and I can see
                                                    the tracks I've
                                                    added.<br>
                                                    <br>
                                                    Now, here is where
                                                    the issue I have
                                                    starts. If I edit
                                                    the <br>
data/nipponbare/tracks.conf file as shown in the dataset selector <br>
                                                    documentation above:<br>
                                                    [general]<br>
                                                    dataset_id =
                                                    nipponbare<br>
                                                    <br>
                                                    Apollo then shows
                                                    the following error:<br>
                                                    Error message(s):<br>
                                                    &nbsp;&nbsp;&nbsp;&nbsp; TypeError:
                                                    Cannot read
                                                    properties of
                                                    undefined (reading
                                                    'name').<br>
                                                    <br>
                                                    Clearing out the
                                                    data/nipponbare/tracks.conf
                                                    file allows apollo
                                                    to work.<br>
                                                    Now, the error only
                                                    appears in apollo,
                                                    jbrowse works fine
                                                    with the edits.<br>
                                                    <br>
                                                    I'm a bit confused
                                                    about how this
                                                    should be configured
                                                    to work. I <br>
                                                    actually have 14
                                                    more &quot;species&quot; to
                                                    add, but waiting
                                                    till I at least get
                                                    <br>
                                                    it working with one.
                                                    The documentation
                                                    isn't clear to me on
                                                    the <br>
                                                    difference between
                                                    adding the datasets
                                                    to jbrowse.conf vs <br>
                                                    data/tracks.conf vs
data/(species)/tracks.conf.<br>
                                                    <br>
                                                    Please let me know
                                                    if you need any more
                                                    information.<br>
                                                    <br>
                                                    Thanks,<br>
                                                    Justin<br>
                                                    <br>
                                                    -- <br>
**********************************************************<br>
                                                    *&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                                                    &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                                                    &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; *<br>
                                                    *&nbsp; Justin Elser&nbsp; &nbsp; &nbsp;
                                                    &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                                                    &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; *<br>
                                                    *&nbsp; Computational
                                                    Biology Research
                                                    Associate&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                                                    &nbsp; *<br>
                                                    *&nbsp; Dept. of Botany
                                                    and Plant Pathology&nbsp;
                                                    &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;*<br>
                                                    *&nbsp; Jaiswal Lab&nbsp; &nbsp; &nbsp;
                                                    &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                                                    &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;*<br>
                                                    *&nbsp; Oregon State
                                                    University&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                                                    &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                                                    &nbsp;*<br>
                                                    *&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                                                    &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                                                    &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; *<br>
                                                    *&nbsp; email: <a href="mailto:jus...@or..." rel="noreferrer
                                                      noreferrer
                                                      noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">
jus...@or...</a>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;*<br>
                                                    *&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                                                    &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                                                    &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; *<br>
**********************************************************<br>
                                                    <br>
                                                    <br>
                                                    <br>
_______________________________________________<br>
                                                    Gmod-ajax mailing
                                                    list<br>
                                                    <a href="mailto:Gmo...@li..." rel="noreferrer
                                                      noreferrer
                                                      noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">Gmo...@li...</a><br>
                                                    <a href="https://lists.sourceforge.net/lists/listinfo/gmod-ajax" originalsrc="https://lists.sourceforge.net/lists/listinfo/gmod-ajax" shash="hvejOAKu6wDQj/B3iauaEHuEeOS4V0fQdAWIgA96Z1DMnTavwMpjgwKd5jEOvjO7OEh9Om9L5a+OaBnsZwdCxPy906PRvhsV77hBuKNZtvyvzy4G/V6dy5PsxA8DmsDEnAUyYZFFrkq0vxVAZ9M3Dnn+NR+NrMuDsyBHGhUYjtA=" rel="noreferrer
                                                      noreferrer
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                                                      Safelink" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">https://lists.sourceforge.net/lists/listinfo/gmod-ajax</a><br>
                                                  </blockquote>
                                                </div>
                                              </div>
                                            </blockquote>
                                            <br>
                                            <pre cols="72">-- 
**********************************************************
*                                                        *
*  Justin Elser                                          *
*  Computational Biology Research Associate              *
*  Dept. of Botany and Plant Pathology                   *
*  Jaiswal Lab                                           *
*  Oregon State University                               *
*                                                        *
*  email: <a href="mailto:jus...@or..." rel="noreferrer noreferrer noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>                   *
*                                                        *
**********************************************************
</pre>
                                          </div>
                                        </blockquote>
                                      </div>
                                    </div>
                                  </blockquote>
                                  <br>
                                  <pre cols="72">-- 
**********************************************************
*                                                        *
*  Justin Elser                                          *
*  Computational Biology Research Associate              *
*  Dept. of Botany and Plant Pathology                   *
*  Jaiswal Lab                                           *
*  Oregon State University                               *
*                                                        *
*  email: <a href="mailto:jus...@or..." rel="noreferrer noreferrer noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>                   *
*                                                        *
**********************************************************
</pre>
                                </div>
                              </blockquote>
                            </div>
                          </div>
                        </blockquote>
                        <br>
                        <pre cols="72">-- 
**********************************************************
*                                                        *
*  Justin Elser                                          *
*  Computational Biology Research Associate              *
*  Dept. of Botany and Plant Pathology                   *
*  Jaiswal Lab                                           *
*  Oregon State University                               *
*                                                        *
*  email: <a href="mailto:jus...@or..." target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>                   *
*                                                        *
**********************************************************
</pre>
                      </div>
                    </blockquote>
                  </div>
                </div>
              </blockquote>
              <br>
              <pre cols="72">-- 
**********************************************************
*                                                        *
*  Justin Elser                                          *
*  Computational Biology Research Associate              *
*  Dept. of Botany and Plant Pathology                   *
*  Jaiswal Lab                                           *
*  Oregon State University                               *
*                                                        *
*  email: <a href="mailto:jus...@or..." target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>                   *
*                                                        *
**********************************************************
</pre>
            </div>
          </blockquote>
        </div>
      </div>
    </blockquote>
    <br>
    <pre class="moz-signature" cols="72">-- 
**********************************************************
*                                                        *
*  Justin Elser                                          *
*  Computational Biology Research Associate              *
*  Dept. of Botany and Plant Pathology                   *
*  Jaiswal Lab                                           *
*  Oregon State University                               *
*                                                        *
*  email: <a class="moz-txt-link-abbreviated" href="mailto:jus...@or...">jus...@or...</a>                   *
*                                                        *
**********************************************************
</pre>
  </body>
</html>

Re: [Gmod-ajax] JBrowse2 CRAM rendering problem after upgrade to 1.6.4

[Colin <col...@gm...>]

Thanks for pointing this out, there was a regression where the fix for this
got undone. Will post a fix soon!

-Colin

On Wed, Jun 1, 2022 at 12:48 PM Ke Jiang <bio...@gm...> wrote:

> Hi,
>
> After upgrading to 1.7.8, this problem seems to be back. In both Firefox
> and Safari, the coverage part of the CRAM rendering would give a reload
> error: "TypeError: e.bezierCurveTo is not a function". Maybe the "sushimi"
> code is not compatible with some recent updates?
>
> Thanks!
>
> Ke
>
> On Fri, Feb 18, 2022 at 3:13 PM Colin <col...@gm...> wrote:
>
>> Fix released in 1.6.5 :)
>>
>> Thanks again for reporting!
>>
>>
>> -Colin
>>
>> On Wed, Feb 16, 2022 at 3:45 PM Colin <col...@gm...> wrote:
>>
>>> Excellent, thank you for reporting the issue! We should have a new
>>> version out soon
>>>
>>>
>>> -Colin
>>>
>>> On Wed, Feb 16, 2022 at 3:02 PM Ke Jiang <bio...@gm...> wrote:
>>>
>>>> Hi, Colin,
>>>>
>>>> Thanks for the quick response. I saw this error with both Safari and
>>>> Firefox. Now you mention the rendering issue with the intron lines, I did
>>>> notice that a while ago. The distinction between BAM and CRAM mentioned in
>>>> the original email was not accurate. The error not showing up for the BAM
>>>> tracks was because the coverage was continuous in the WGS data, which
>>>> happens to be using BAM, while the RNA-Seq data with introns/gaps happens
>>>> to be CRAM files.
>>>>
>>>> Thank you very much for fixing this! Since it was a small glitch for
>>>> alignment tracks only, I think I'll wait for 1.6.5 to upgrade.
>>>>
>>>> Best.
>>>>
>>>> Ke
>>>>
>>>> On Tue, Feb 15, 2022 at 6:22 PM Colin <col...@gm...> wrote:
>>>>
>>>>> Hi Ke,
>>>>> This is an interesting error. The issue would probably be related to
>>>>> the new rendering of the "sashimi" style arcs introduced in 1.5.2 (
>>>>> https://jbrowse.org/jb2/blog/2021/12/20/v1.5.2-release/) but I have
>>>>> not seen this error.
>>>>>
>>>>> Can you tell me what browser you are using?
>>>>>
>>>>>
>>>>> I found what I think is a fix here
>>>>> https://github.com/GMOD/jbrowse-components/pull/2750 but I would
>>>>> still like to know more info because there are also some possible rendering
>>>>> glitches in your screenshot (looks like some "intron" lines are drawn on
>>>>> top of features). If you have data that reproduces this let me know
>>>>>
>>>>>
>>>>> -Colin
>>>>>
>>>>>
>>>>>
>>>>> On Tue, Feb 15, 2022 at 2:31 PM Ke Jiang <bio...@gm...> wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> After upgrading to 1.6.4, the CRAM tracks give an error
>>>>>> ("e.bezierCurveTo is nor function") when rendering coverage plots (the BAM
>>>>>> tracks are fine), the read alignment rendering part seems to be fine. Here
>>>>>> is a screenshot and configuration. I'd like to put it here before taking it
>>>>>> to github issues, maybe there is a simple fix or configuration error on my
>>>>>> side.
>>>>>>
>>>>>> Thanks!
>>>>>>
>>>>>> Ke
>>>>>>
>>>>>> [image: ScreenShot.png]
>>>>>>
>>>>>>
>>>>>> {
>>>>>>       "type": "AlignmentsTrack",
>>>>>>       "trackId": "SRR11185046_reads",
>>>>>>       "name": "SRR11185046",
>>>>>>       "category": [
>>>>>>         "mRNASeq"
>>>>>>       ],
>>>>>>       "assemblyNames": [
>>>>>>         "Porcine S. scrofa v11.1"
>>>>>>       ],
>>>>>>       "adapter": {
>>>>>>         "type": "CramAdapter",
>>>>>>         "cramLocation": {
>>>>>>           "uri": "data/porcine/Sscrofa11/mRNASeq/SRR11185046.cram"
>>>>>>         },
>>>>>>         "craiLocation": {
>>>>>>           "uri":
>>>>>> "data/porcine/Sscrofa11/mRNASeq/SRR11185046.cram.crai"
>>>>>>         },
>>>>>>         "sequenceAdapter": {
>>>>>>           "type": "IndexedFastaAdapter",
>>>>>>           "fastaLocation": {
>>>>>>             "uri": "Sscrofa11.1.fa"
>>>>>>           },
>>>>>>           "faiLocation": {
>>>>>>             "uri": "Sscrofa11.1.fa.fai"
>>>>>>           }
>>>>>>         }
>>>>>>       }
>>>>>>     },
>>>>>> _______________________________________________
>>>>>> Gmod-ajax mailing list
>>>>>> Gmo...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>>>
>>>>>

Re: [Gmod-ajax] JBrowse2 CRAM rendering problem after upgrade to 1.6.4

[Ke J. <bio...@gm...>]

Hi,

After upgrading to 1.7.8, this problem seems to be back. In both Firefox
and Safari, the coverage part of the CRAM rendering would give a reload
error: "TypeError: e.bezierCurveTo is not a function". Maybe the "sushimi"
code is not compatible with some recent updates?

Thanks!

Ke

On Fri, Feb 18, 2022 at 3:13 PM Colin <col...@gm...> wrote:

> Fix released in 1.6.5 :)
>
> Thanks again for reporting!
>
>
> -Colin
>
> On Wed, Feb 16, 2022 at 3:45 PM Colin <col...@gm...> wrote:
>
>> Excellent, thank you for reporting the issue! We should have a new
>> version out soon
>>
>>
>> -Colin
>>
>> On Wed, Feb 16, 2022 at 3:02 PM Ke Jiang <bio...@gm...> wrote:
>>
>>> Hi, Colin,
>>>
>>> Thanks for the quick response. I saw this error with both Safari and
>>> Firefox. Now you mention the rendering issue with the intron lines, I did
>>> notice that a while ago. The distinction between BAM and CRAM mentioned in
>>> the original email was not accurate. The error not showing up for the BAM
>>> tracks was because the coverage was continuous in the WGS data, which
>>> happens to be using BAM, while the RNA-Seq data with introns/gaps happens
>>> to be CRAM files.
>>>
>>> Thank you very much for fixing this! Since it was a small glitch for
>>> alignment tracks only, I think I'll wait for 1.6.5 to upgrade.
>>>
>>> Best.
>>>
>>> Ke
>>>
>>> On Tue, Feb 15, 2022 at 6:22 PM Colin <col...@gm...> wrote:
>>>
>>>> Hi Ke,
>>>> This is an interesting error. The issue would probably be related to
>>>> the new rendering of the "sashimi" style arcs introduced in 1.5.2 (
>>>> https://jbrowse.org/jb2/blog/2021/12/20/v1.5.2-release/) but I have
>>>> not seen this error.
>>>>
>>>> Can you tell me what browser you are using?
>>>>
>>>>
>>>> I found what I think is a fix here
>>>> https://github.com/GMOD/jbrowse-components/pull/2750 but I would still
>>>> like to know more info because there are also some possible rendering
>>>> glitches in your screenshot (looks like some "intron" lines are drawn on
>>>> top of features). If you have data that reproduces this let me know
>>>>
>>>>
>>>> -Colin
>>>>
>>>>
>>>>
>>>> On Tue, Feb 15, 2022 at 2:31 PM Ke Jiang <bio...@gm...> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> After upgrading to 1.6.4, the CRAM tracks give an error
>>>>> ("e.bezierCurveTo is nor function") when rendering coverage plots (the BAM
>>>>> tracks are fine), the read alignment rendering part seems to be fine. Here
>>>>> is a screenshot and configuration. I'd like to put it here before taking it
>>>>> to github issues, maybe there is a simple fix or configuration error on my
>>>>> side.
>>>>>
>>>>> Thanks!
>>>>>
>>>>> Ke
>>>>>
>>>>> [image: ScreenShot.png]
>>>>>
>>>>>
>>>>> {
>>>>>       "type": "AlignmentsTrack",
>>>>>       "trackId": "SRR11185046_reads",
>>>>>       "name": "SRR11185046",
>>>>>       "category": [
>>>>>         "mRNASeq"
>>>>>       ],
>>>>>       "assemblyNames": [
>>>>>         "Porcine S. scrofa v11.1"
>>>>>       ],
>>>>>       "adapter": {
>>>>>         "type": "CramAdapter",
>>>>>         "cramLocation": {
>>>>>           "uri": "data/porcine/Sscrofa11/mRNASeq/SRR11185046.cram"
>>>>>         },
>>>>>         "craiLocation": {
>>>>>           "uri": "data/porcine/Sscrofa11/mRNASeq/SRR11185046.cram.crai"
>>>>>         },
>>>>>         "sequenceAdapter": {
>>>>>           "type": "IndexedFastaAdapter",
>>>>>           "fastaLocation": {
>>>>>             "uri": "Sscrofa11.1.fa"
>>>>>           },
>>>>>           "faiLocation": {
>>>>>             "uri": "Sscrofa11.1.fa.fai"
>>>>>           }
>>>>>         }
>>>>>       }
>>>>>     },
>>>>> _______________________________________________
>>>>> Gmod-ajax mailing list
>>>>> Gmo...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>>
>>>>

[Gmod-ajax] JBrowse XML parsing errors

[Vaneet L. <van...@uc...>]

Hi,

I attached a screenshot of the XML parsing errors from the console of my Firefox browser, which I'm a little confused about.  I checked the actual configuration files that these errors denote, and I don't see anything wrong or any hidden characters that are there on the first line.  I don't think these are file specific though as no matter what genome I switch to in JBrowse I see the same errors, that is those genomes for which I have an extra configuration file for functions that's named 'functions.conf'.  The jbrowse.conf error always appears.  I don't see any visible problem on the browser tracks that results from these errors but I just want to eliminate them to make sure.

After looking at the JBrowse 1 troubleshooting page, I took the suggestion to install the libexpat1-dev package and then rerun the setup.sh script, but errors are still there on Firefox.  If I load the page in Microsoft Edge browser, I don't see the errors there, so I'm wondering if it's browser specific? Is anyone aware of any fixes for this specific issue?

Thanks,

Vaneet

Re: [Gmod-ajax] Dataset selector in apollo

[Colin <col...@gm...>]

>Everything works as expected now! I see both Nipponbare and ARC in the
"Genome" dropdown, and apollo is showing all data.

Excellent:)

>So, I guess apollo is only using the numeric ID for the dataset instead of
using what I tried to set the dataset id? In other words, if I had
[datasets.nipponbare] in jbrowse.conf and dataset_id=nipponbare in
data/nipponbare/tracks.conf, that is fine for jbrowse, but apollo is only
using it's internal ID of 34?

You can inspect the database for the IDs, or you can get the ID from inside
the URL clicking the link icon, see screenshot attachment here. I don't
think you can change the organism ID to something else like a readable name
unfortunately.

-Colin

On Thu, May 26, 2022 at 12:24 PM Justin Elser <jus...@or...>
wrote:

> Ok, I think I get it. At least, I think I can get it working but I am a
> bit confused.
>
> So, I noticed in the apollo docker logs that I see this:
> 2022-05-26 18:10:34,589 [http-nio-8080-exec-4] DEBUG
> apollo.PreferenceService  - found organism in session
> org.bbop.apollo.Organism : 34 so returning
> 2022-05-26 18:10:34,589 [http-nio-8080-exec-4] DEBUG
> apollo.JbrowseController  - got organism org.bbop.apollo.Organism : 34 for
> client token 137967108160676781264638533
> 2022-05-26 18:10:34,649 [http-nio-8080-exec-1] DEBUG
> apollo.AnnotationEditorController  - handleOperation annotationEditor
> get_sequence_alterations -> getSequenceAlterations
> 2022-05-26 18:10:34,650 [http-nio-8080-exec-1] DEBUG
> apollo.PermissionService  - dataObject does not contain organism (may not
> be needed)
> 2022-05-26 18:10:34,652 [http-nio-8080-exec-1] DEBUG
> apollo.PreferenceService  - found in-memory preference:
> {"id":96,"organism":{"id":34,"commonName":"Nipponbare","directory":"/data/nipponbare","annotationCount":null,"variantEffectCount":null,"officialGeneSetTrack":null},"currentOrganism":true,"nativeTrackList":true,"sequence":{"id":36,"name":"chr1","organism":{"id":34,"commonName":"Nipponbare","directory":"/data/nipponbare","annotationCount":null,"variantEffectCount":null,"officialGeneSetTrack":null},"length":43270923,"start":0,"end":43270923},"startbp":6587035,"endbp":7241056,"clientToken":"137967108160676781264638533","user":{"id":32,"username":
> "admin@local.host" <admin@local.host>}}
>
> So, it looks like the apollo "id" is 34 for Nipponbare, and similarly 51
> for ARC.
>
> So, I changed the jbrowse.conf to have:
> [datasets.34]
> url = ?data=data/nipponbare
> name = Nipponbare
> [datasets.51]
> url = ?data=data/arc
> name = ARC
> and data/nipponbare/tracks.conf to have:
> [general]
> dataset_id = 34
>
> and similar change for data/arc/tracks.conf.
>
> Everything works as expected now! I see both Nipponbare and ARC in the
> "Genome" dropdown, and apollo is showing all data.
>
> So, I guess apollo is only using the numeric ID for the dataset instead of
> using what I tried to set the dataset id? In other words, if I had
> [datasets.nipponbare] in jbrowse.conf and dataset_id=nipponbare in
> data/nipponbare/tracks.conf, that is fine for jbrowse, but apollo is only
> using it's internal ID of 34?
>
> I guess I just don't understand why apollo isn't seeing the dataset_id I'm
> trying to set in jbrowse instead of seeing it's own ID.
>
> How can I see what ID apollo is going to use without just checking the
> logs and seeing what it looks for? Or can I force it somehow to use
> nipponbare instead of 34?
>
> Thanks for the info on JBrowse2/Apollo3, I'll watch for updates.
>
> Justin
>
> On 5/26/22 11:00 AM, Colin wrote:
>
> [This email originated from outside of OSU. Use caution with links and
> attachments.]
> The code that is crashing is probably this, seeing renderDatasetSelector
> in the stack trace
>
>
> https://github.com/GMOD/jbrowse/blob/fd7ebb8a0802db9e09ac34c70689e7a9cfccc615/src/JBrowse/Browser.js#L1214-L1216
>
> Since it is crashing there, I think maybe your manually configured
> datasets are not matching the Apollo configuration of the datasets.
>
> If you make them match up, it might fix it, and to do that, you may be
> able to make the dataset ID be the organism ID that Apollo gives. Would
> have to update both the datasets and the dataset_id
>
> This is where Apollo sets the dataset_id, uses organism ID
> https://github.com/GMOD/Apollo/blob/1728c280f9a18bd22e07f8b4b9f00a8e24432358/grails-app/controllers/org/bbop/apollo/JbrowseController.groovy#L435-L440
>
> To be clear, the dataset ID is what is after the . in the conf format e.g.
>
> [datasets.make_this_match_the_organismID]
> url = ?data=data/nipponbare
> name = Nipponbare
>
>
> Also, the current generation of Apollo (Apollo 2) does not work with
> JBrowse 2, but we are working on a new Apollo version that will be
> integrated with JBrowse 2. It's not ready for use yet but you can keep an
> eye on https://github.com/GMOD/Apollo3 if interested
>
> -Colin
>
>
>
> On Thu, May 26, 2022 at 9:56 AM Justin Elser <jus...@or...>
> wrote:
>
>> I'm attaching the output from the chrome console. I don't think it's the
>> non-minified version of the JS though. How would I get that with the docker
>> version of apollo?
>>
>> Also, I've been asked to ask if Apollo works with JBrowse2? Would it be
>> better to use that instead of JBrowse1?
>>
>> Thank you for taking the time to help me.
>>
>> Justin
>>
>> On 5/25/22 4:51 PM, Colin wrote:
>>
>> [This email originated from outside of OSU. Use caution with links and
>> attachments.]
>> The logs that are probably most helpful are the "JavaScript console" or
>> developer console from chrome or firefox e.g.
>> https://balsamiq.com/support/faqs/browserconsole/
>>
>> On Wed, May 25, 2022, 4:33 PM Justin Elser <jus...@or...>
>> wrote:
>>
>>> We may just use Apollo to serve both, but thought I might give it a try
>>> to see about JBrowse.
>>>
>>> I am attaching the output I get when I run the docker container with "-e
>>> WEBAPOLLO_DEBUG=true".
>>>
>>> The blank lines are in between it working and not working. IE, lines
>>> 1-483 are the initial startup and navigating to the site with Apollo
>>> working as expected. Lines 487 on are after changing
>>> data/nipponbare/tracks.conf to have:
>>> [general]
>>> dataset_id = nipponbare
>>>
>>> I do notice that after the change it is trying to open
>>> /data/temporary/apollo_data/34-Nipponbare/sample_data/json/volvox/successfully_run
>>> (line 579) where it isn't before. I don't understand why it would be
>>> looking for the sample data at all. I never loaded it as a track or
>>> anything.
>>>
>>> I also notice for the initial load where it works that it is complaining
>>> about the mime_type for .bam files. I did alter the .htaccess for the
>>> jbrowse but not apollo, so I think those are fixable and unrelated. Weirdly
>>> enough, the bam track does load fine in Apollo where it didn't in JBrowse
>>> until I made the change to .htaccess.
>>>
>>> If you meant some other logs, please let me know how to get those and I
>>> will send them to you.
>>>
>>> Thanks,
>>> Justin
>>>
>>> On 5/25/22 2:18 PM, Colin wrote:
>>>
>>> [This email originated from outside of OSU. Use caution with links and
>>> attachments.]
>>> One option is to use Apollo to serve your jbrowse instances, Apollo can
>>> serve public jbrowse instances so you may not need to configure jbrowse
>>> separately
>>>
>>>
>>> If you do want it separate, then we would probably need to debug that
>>> error. If you have the stack trace from the developer console, it might
>>> narrow down exactly where the error comes from. If the stack trace is
>>> minified and hard to read, can possibly use a "dev" version of jbrowse if
>>> it is too unreadable since it does not minify the builds!
>>>
>>>
>>>
>>> -Colin
>>>
>>> On Wed, May 25, 2022 at 1:03 PM Justin Elser <
>>> jus...@or...> wrote:
>>>
>>>> Yeah, so I guess the problem is that if I don't add the "dataset_id" to
>>>> each data/(species)/tracks.conf file, apollo works fine, but then I can't
>>>> get the dataset selector in jbrowse. As I have it right now, Apollo is
>>>> fine, but I have no way to switch to a different dataset in JBrowse.
>>>>
>>>>
>>>> I was messing around with jbrowse.conf, data/tracks.conf, and
>>>> data/(species)/tracks.conf, and was able to get a list of the species under
>>>> the "Genome" tab. But if I don't have anything in
>>>> data/(species)/tracks.conf, I don't. However, if I do add it like in the
>>>> documentation, the species are listed under there:
>>>>
>>>> But then, apollo breaks:
>>>>
>>>>
>>>> So, I guess I need to get the dataset_selector working in JBrowse,
>>>> while not breaking Apollo.
>>>>
>>>> I hope that clears it up more.
>>>>
>>>> Thanks,
>>>> Justin
>>>>
>>>> On 5/25/22 11:50 AM, Colin wrote:
>>>>
>>>> [This email originated from outside of OSU. Use caution with links and
>>>> attachments.]
>>>> I haven't evaluated the whole post here, but note that Apollo
>>>> automatically creates a dataset selector from assemblies that you configure
>>>> through that Apollo interface
>>>>
>>>>
>>>> -Colin
>>>>
>>>> On Wed, May 25, 2022 at 12:21 PM Justin Elser <
>>>> jus...@or...> wrote:
>>>>
>>>>> Hi all,
>>>>>
>>>>> I have set up a jbrowse 1.16.11 instance (sorry, not publicly
>>>>> available)
>>>>> and added 2 species (well, different cultivars) by doing the following:
>>>>> bin/prepare-refseqs.pl --out data/nipponbare --fasta
>>>>> source_files/RAPDB-Reference-Nipponbare_chr_fixed.fasta
>>>>> bin/flatfile-to-json.pl --out data/nipponbare --trackType
>>>>> CanvasFeatures
>>>>> --trackLabel MSU7.0 -gff source_files/MSU7.0.gff3
>>>>> bin/generate-names.pl --out data/nipponbare
>>>>>
>>>>> bin/prepare-refseqs.pl --out data/arc --fasta
>>>>> source_files/magic_16/oryza_sativa_arc.fa
>>>>> bin/flatfile-to-json.pl --out data/arc --trackType CanvasFeatures
>>>>> --trackLabel Genes -gff source_files/magic_16/oryza_sativa_arc.gff
>>>>> bin/generate-names.pl --out data/arc
>>>>>
>>>>> Then I edited the jbrowse.conf file as explained in
>>>>> https://jbrowse.org/docs/dataset_selector.html to have:
>>>>> dataRoot = data/nipponbare
>>>>> [datasets.nipponbare]
>>>>> url = ?data=data/nipponbare
>>>>> name = Nipponbare
>>>>> [datasets.arc]
>>>>> url = ?data=data/arc
>>>>> name = ARC
>>>>>
>>>>> And all seems to work fine, except that I don't see the dropdown to
>>>>> switch datasets, so I can't actually see the ARC dataset. Although I
>>>>> have by messing around with jbrowse.conf and tracks.conf gotten it to
>>>>> work, but at this point I've left it out.
>>>>>
>>>>> However, the issue I'm having is actually with Apollo. I have the
>>>>> docker
>>>>> instance of apollo running and it seems to be fine as configured in a
>>>>> systemd unit file:
>>>>> ExecStart=/usr/bin/docker run --rm --name %n \
>>>>>          -e APOLLO_PATH=apollo \
>>>>>          -v /data/www/panoryza/jbrowse/data:/data \
>>>>>          -v /data/www/panoryza/apollo/postgres:/var/lib/postgresql \
>>>>>          -v
>>>>> /data/www/panoryza/apollo/apollo_data:/data/temporary/apollo_data \
>>>>>          -p 8887:8080 \
>>>>>          gmod/apollo:latest
>>>>>
>>>>> Adding Nipponbare as an organism with "Directory" /data/nipponbare
>>>>> works
>>>>> fine and I can see the tracks I've added.
>>>>>
>>>>> Now, here is where the issue I have starts. If I edit the
>>>>> data/nipponbare/tracks.conf file as shown in the dataset selector
>>>>> documentation above:
>>>>> [general]
>>>>> dataset_id = nipponbare
>>>>>
>>>>> Apollo then shows the following error:
>>>>> Error message(s):
>>>>>      TypeError: Cannot read properties of undefined (reading 'name').
>>>>>
>>>>> Clearing out the data/nipponbare/tracks.conf file allows apollo to
>>>>> work.
>>>>> Now, the error only appears in apollo, jbrowse works fine with the
>>>>> edits.
>>>>>
>>>>> I'm a bit confused about how this should be configured to work. I
>>>>> actually have 14 more "species" to add, but waiting till I at least
>>>>> get
>>>>> it working with one. The documentation isn't clear to me on the
>>>>> difference between adding the datasets to jbrowse.conf vs
>>>>> data/tracks.conf vs data/(species)/tracks.conf.
>>>>>
>>>>> Please let me know if you need any more information.
>>>>>
>>>>> Thanks,
>>>>> Justin
>>>>>
>>>>> --
>>>>> **********************************************************
>>>>> *                                                        *
>>>>> *  Justin Elser                                          *
>>>>> *  Computational Biology Research Associate              *
>>>>> *  Dept. of Botany and Plant Pathology                   *
>>>>> *  Jaiswal Lab                                           *
>>>>> *  Oregon State University                               *
>>>>> *                                                        *
>>>>> *  email: jus...@or...                   *
>>>>> *                                                        *
>>>>> **********************************************************
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Gmod-ajax mailing list
>>>>> Gmo...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>>
>>>>
>>>> --
>>>> **********************************************************
>>>> *                                                        *
>>>> *  Justin Elser                                          *
>>>> *  Computational Biology Research Associate              *
>>>> *  Dept. of Botany and Plant Pathology                   *
>>>> *  Jaiswal Lab                                           *
>>>> *  Oregon State University                               *
>>>> *                                                        *
>>>> *  email: jus...@or...                   *
>>>> *                                                        *
>>>> **********************************************************
>>>>
>>>>
>>> --
>>> **********************************************************
>>> *                                                        *
>>> *  Justin Elser                                          *
>>> *  Computational Biology Research Associate              *
>>> *  Dept. of Botany and Plant Pathology                   *
>>> *  Jaiswal Lab                                           *
>>> *  Oregon State University                               *
>>> *                                                        *
>>> *  email: jus...@or...                   *
>>> *                                                        *
>>> **********************************************************
>>>
>>>
>> --
>> **********************************************************
>> *                                                        *
>> *  Justin Elser                                          *
>> *  Computational Biology Research Associate              *
>> *  Dept. of Botany and Plant Pathology                   *
>> *  Jaiswal Lab                                           *
>> *  Oregon State University                               *
>> *                                                        *
>> *  email: jus...@or...                   *
>> *                                                        *
>> **********************************************************
>>
>>
> --
> **********************************************************
> *                                                        *
> *  Justin Elser                                          *
> *  Computational Biology Research Associate              *
> *  Dept. of Botany and Plant Pathology                   *
> *  Jaiswal Lab                                           *
> *  Oregon State University                               *
> *                                                        *
> *  email: jus...@or...                   *
> *                                                        *
> **********************************************************
>
>

Re: [Gmod-ajax] Dataset selector in apollo

[Colin <col...@gm...>]

The code that is crashing is probably this, seeing renderDatasetSelector in
the stack trace

https://github.com/GMOD/jbrowse/blob/fd7ebb8a0802db9e09ac34c70689e7a9cfccc615/src/JBrowse/Browser.js#L1214-L1216

Since it is crashing there, I think maybe your manually configured
datasets are not matching the Apollo configuration of the datasets.

If you make them match up, it might fix it, and to do that, you may be able
to make the dataset ID be the organism ID that Apollo gives. Would have to
update both the datasets and the dataset_id

This is where Apollo sets the dataset_id, uses organism ID
https://github.com/GMOD/Apollo/blob/1728c280f9a18bd22e07f8b4b9f00a8e24432358/grails-app/controllers/org/bbop/apollo/JbrowseController.groovy#L435-L440

To be clear, the dataset ID is what is after the . in the conf format e.g.

[datasets.make_this_match_the_organismID]
url = ?data=data/nipponbare
name = Nipponbare


Also, the current generation of Apollo (Apollo 2) does not work with
JBrowse 2, but we are working on a new Apollo version that will be
integrated with JBrowse 2. It's not ready for use yet but you can keep an
eye on https://github.com/GMOD/Apollo3 if interested

-Colin



On Thu, May 26, 2022 at 9:56 AM Justin Elser <jus...@or...>
wrote:

> I'm attaching the output from the chrome console. I don't think it's the
> non-minified version of the JS though. How would I get that with the docker
> version of apollo?
>
> Also, I've been asked to ask if Apollo works with JBrowse2? Would it be
> better to use that instead of JBrowse1?
>
> Thank you for taking the time to help me.
>
> Justin
>
> On 5/25/22 4:51 PM, Colin wrote:
>
> [This email originated from outside of OSU. Use caution with links and
> attachments.]
> The logs that are probably most helpful are the "JavaScript console" or
> developer console from chrome or firefox e.g.
> https://balsamiq.com/support/faqs/browserconsole/
>
> On Wed, May 25, 2022, 4:33 PM Justin Elser <jus...@or...>
> wrote:
>
>> We may just use Apollo to serve both, but thought I might give it a try
>> to see about JBrowse.
>>
>> I am attaching the output I get when I run the docker container with "-e
>> WEBAPOLLO_DEBUG=true".
>>
>> The blank lines are in between it working and not working. IE, lines
>> 1-483 are the initial startup and navigating to the site with Apollo
>> working as expected. Lines 487 on are after changing
>> data/nipponbare/tracks.conf to have:
>> [general]
>> dataset_id = nipponbare
>>
>> I do notice that after the change it is trying to open
>> /data/temporary/apollo_data/34-Nipponbare/sample_data/json/volvox/successfully_run
>> (line 579) where it isn't before. I don't understand why it would be
>> looking for the sample data at all. I never loaded it as a track or
>> anything.
>>
>> I also notice for the initial load where it works that it is complaining
>> about the mime_type for .bam files. I did alter the .htaccess for the
>> jbrowse but not apollo, so I think those are fixable and unrelated. Weirdly
>> enough, the bam track does load fine in Apollo where it didn't in JBrowse
>> until I made the change to .htaccess.
>>
>> If you meant some other logs, please let me know how to get those and I
>> will send them to you.
>>
>> Thanks,
>> Justin
>>
>> On 5/25/22 2:18 PM, Colin wrote:
>>
>> [This email originated from outside of OSU. Use caution with links and
>> attachments.]
>> One option is to use Apollo to serve your jbrowse instances, Apollo can
>> serve public jbrowse instances so you may not need to configure jbrowse
>> separately
>>
>>
>> If you do want it separate, then we would probably need to debug that
>> error. If you have the stack trace from the developer console, it might
>> narrow down exactly where the error comes from. If the stack trace is
>> minified and hard to read, can possibly use a "dev" version of jbrowse if
>> it is too unreadable since it does not minify the builds!
>>
>>
>>
>> -Colin
>>
>> On Wed, May 25, 2022 at 1:03 PM Justin Elser <
>> jus...@or...> wrote:
>>
>>> Yeah, so I guess the problem is that if I don't add the "dataset_id" to
>>> each data/(species)/tracks.conf file, apollo works fine, but then I can't
>>> get the dataset selector in jbrowse. As I have it right now, Apollo is
>>> fine, but I have no way to switch to a different dataset in JBrowse.
>>>
>>>
>>> I was messing around with jbrowse.conf, data/tracks.conf, and
>>> data/(species)/tracks.conf, and was able to get a list of the species under
>>> the "Genome" tab. But if I don't have anything in
>>> data/(species)/tracks.conf, I don't. However, if I do add it like in the
>>> documentation, the species are listed under there:
>>>
>>> But then, apollo breaks:
>>>
>>>
>>> So, I guess I need to get the dataset_selector working in JBrowse, while
>>> not breaking Apollo.
>>>
>>> I hope that clears it up more.
>>>
>>> Thanks,
>>> Justin
>>>
>>> On 5/25/22 11:50 AM, Colin wrote:
>>>
>>> [This email originated from outside of OSU. Use caution with links and
>>> attachments.]
>>> I haven't evaluated the whole post here, but note that Apollo
>>> automatically creates a dataset selector from assemblies that you configure
>>> through that Apollo interface
>>>
>>>
>>> -Colin
>>>
>>> On Wed, May 25, 2022 at 12:21 PM Justin Elser <
>>> jus...@or...> wrote:
>>>
>>>> Hi all,
>>>>
>>>> I have set up a jbrowse 1.16.11 instance (sorry, not publicly
>>>> available)
>>>> and added 2 species (well, different cultivars) by doing the following:
>>>> bin/prepare-refseqs.pl --out data/nipponbare --fasta
>>>> source_files/RAPDB-Reference-Nipponbare_chr_fixed.fasta
>>>> bin/flatfile-to-json.pl --out data/nipponbare --trackType
>>>> CanvasFeatures
>>>> --trackLabel MSU7.0 -gff source_files/MSU7.0.gff3
>>>> bin/generate-names.pl --out data/nipponbare
>>>>
>>>> bin/prepare-refseqs.pl --out data/arc --fasta
>>>> source_files/magic_16/oryza_sativa_arc.fa
>>>> bin/flatfile-to-json.pl --out data/arc --trackType CanvasFeatures
>>>> --trackLabel Genes -gff source_files/magic_16/oryza_sativa_arc.gff
>>>> bin/generate-names.pl --out data/arc
>>>>
>>>> Then I edited the jbrowse.conf file as explained in
>>>> https://jbrowse.org/docs/dataset_selector.html to have:
>>>> dataRoot = data/nipponbare
>>>> [datasets.nipponbare]
>>>> url = ?data=data/nipponbare
>>>> name = Nipponbare
>>>> [datasets.arc]
>>>> url = ?data=data/arc
>>>> name = ARC
>>>>
>>>> And all seems to work fine, except that I don't see the dropdown to
>>>> switch datasets, so I can't actually see the ARC dataset. Although I
>>>> have by messing around with jbrowse.conf and tracks.conf gotten it to
>>>> work, but at this point I've left it out.
>>>>
>>>> However, the issue I'm having is actually with Apollo. I have the
>>>> docker
>>>> instance of apollo running and it seems to be fine as configured in a
>>>> systemd unit file:
>>>> ExecStart=/usr/bin/docker run --rm --name %n \
>>>>          -e APOLLO_PATH=apollo \
>>>>          -v /data/www/panoryza/jbrowse/data:/data \
>>>>          -v /data/www/panoryza/apollo/postgres:/var/lib/postgresql \
>>>>          -v
>>>> /data/www/panoryza/apollo/apollo_data:/data/temporary/apollo_data \
>>>>          -p 8887:8080 \
>>>>          gmod/apollo:latest
>>>>
>>>> Adding Nipponbare as an organism with "Directory" /data/nipponbare
>>>> works
>>>> fine and I can see the tracks I've added.
>>>>
>>>> Now, here is where the issue I have starts. If I edit the
>>>> data/nipponbare/tracks.conf file as shown in the dataset selector
>>>> documentation above:
>>>> [general]
>>>> dataset_id = nipponbare
>>>>
>>>> Apollo then shows the following error:
>>>> Error message(s):
>>>>      TypeError: Cannot read properties of undefined (reading 'name').
>>>>
>>>> Clearing out the data/nipponbare/tracks.conf file allows apollo to work.
>>>> Now, the error only appears in apollo, jbrowse works fine with the
>>>> edits.
>>>>
>>>> I'm a bit confused about how this should be configured to work. I
>>>> actually have 14 more "species" to add, but waiting till I at least get
>>>> it working with one. The documentation isn't clear to me on the
>>>> difference between adding the datasets to jbrowse.conf vs
>>>> data/tracks.conf vs data/(species)/tracks.conf.
>>>>
>>>> Please let me know if you need any more information.
>>>>
>>>> Thanks,
>>>> Justin
>>>>
>>>> --
>>>> **********************************************************
>>>> *                                                        *
>>>> *  Justin Elser                                          *
>>>> *  Computational Biology Research Associate              *
>>>> *  Dept. of Botany and Plant Pathology                   *
>>>> *  Jaiswal Lab                                           *
>>>> *  Oregon State University                               *
>>>> *                                                        *
>>>> *  email: jus...@or...                   *
>>>> *                                                        *
>>>> **********************************************************
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Gmod-ajax mailing list
>>>> Gmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>
>>>
>>> --
>>> **********************************************************
>>> *                                                        *
>>> *  Justin Elser                                          *
>>> *  Computational Biology Research Associate              *
>>> *  Dept. of Botany and Plant Pathology                   *
>>> *  Jaiswal Lab                                           *
>>> *  Oregon State University                               *
>>> *                                                        *
>>> *  email: jus...@or...                   *
>>> *                                                        *
>>> **********************************************************
>>>
>>>
>> --
>> **********************************************************
>> *                                                        *
>> *  Justin Elser                                          *
>> *  Computational Biology Research Associate              *
>> *  Dept. of Botany and Plant Pathology                   *
>> *  Jaiswal Lab                                           *
>> *  Oregon State University                               *
>> *                                                        *
>> *  email: jus...@or...                   *
>> *                                                        *
>> **********************************************************
>>
>>
> --
> **********************************************************
> *                                                        *
> *  Justin Elser                                          *
> *  Computational Biology Research Associate              *
> *  Dept. of Botany and Plant Pathology                   *
> *  Jaiswal Lab                                           *
> *  Oregon State University                               *
> *                                                        *
> *  email: jus...@or...                   *
> *                                                        *
> **********************************************************
>
>

Re: [Gmod-ajax] Dataset selector in apollo

[Justin E. <jus...@or...>]

<html><head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
  </head>
  <body>
    I'm attaching the output from the chrome console. I don't think it's
    the non-minified version of the JS though. How would I get that with
    the docker version of apollo?<br>
    <br>
    Also, I've been asked to ask if Apollo works with JBrowse2? Would it
    be better to use that instead of JBrowse1?<br>
    <br>
    Thank you for taking the time to help me.<br>
    <br>
    Justin<br>
    <br>
    <div class="moz-cite-prefix">On 5/25/22 4:51 PM, Colin wrote:<br>
    </div>
    <blockquote type="cite" cite="mid:CA+...@ma...">
      
      <p><span style="color:#D73F09;">[This email originated from
          outside of OSU. Use caution with links and attachments.]</span></p>
      <div>
        <div dir="auto">The logs that are probably most helpful are the
          &quot;JavaScript console&quot; or developer console from chrome or
          firefox e.g.
          <a href="https://balsamiq.com/support/faqs/browserconsole/" originalsrc="https://balsamiq.com/support/faqs/browserconsole/" shash="aiCz/OnBddYj4od+LOHVXj9Tq5GlWP+IORJqZ7Z7WBgj41oQOhE6mVZWYKNq3E0Kyx93xXSRfQlDQXIRn5/3DI65xgWOCgmuM3HVWxzEAMEGHi4BHvsGl+pzPy81lK3hZKdsSpdeB1zr1lRpwLktCpwpuC3PzjKbGTSE8dJWgcc=" target="_blank" rel="noreferrer" moz-do-not-send="true" title="Unmangled Microsoft Safelink" class="moz-txt-link-freetext">
            https://balsamiq.com/support/faqs/browserconsole/</a></div>
        <br>
        <div class="gmail_quote">
          <div dir="ltr" class="gmail_attr">On Wed, May 25, 2022, 4:33
            PM Justin Elser &lt;<a href="mailto:jus...@or..." rel="noreferrer
              noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>&gt;
            wrote:<br>
          </div>
          <blockquote class="gmail_quote" style="margin:0 0 0
            .8ex;border-left:1px #ccc solid;padding-left:1ex">
            <div>We may just use Apollo to serve both, but thought I
              might give it a try to see about JBrowse.<br>
              <br>
              I am attaching the output I get when I run the docker
              container with &quot;-e WEBAPOLLO_DEBUG=true&quot;.<br>
              <br>
              The blank lines are in between it working and not working.
              IE, lines 1-483 are the initial startup and navigating to
              the site with Apollo working as expected. Lines 487 on are
              after changing data/nipponbare/tracks.conf to have:<br>
              [general]<br>
              dataset_id = nipponbare<br>
              <br>
              I do notice that after the change it is trying to open
/data/temporary/apollo_data/34-Nipponbare/sample_data/json/volvox/successfully_run
              (line 579) where it isn't before. I don't understand why
              it would be looking for the sample data at all. I never
              loaded it as a track or anything.<br>
              <br>
              I also notice for the initial load where it works that it
              is complaining about the mime_type for .bam files. I did
              alter the .htaccess for the jbrowse but not apollo, so I
              think those are fixable and unrelated. Weirdly enough, the
              bam track does load fine in Apollo where it didn't in
              JBrowse until I made the change to .htaccess.<br>
              <br>
              If you meant some other logs, please let me know how to
              get those and I will send them to you.<br>
              <br>
              Thanks,<br>
              Justin<br>
              <br>
              <div>On 5/25/22 2:18 PM, Colin wrote:<br>
              </div>
              <blockquote type="cite">
                <p><span style="color:#d73f09">[This email originated
                    from outside of OSU. Use caution with links and
                    attachments.]</span></p>
                <div>
                  <div dir="ltr">One option is to use Apollo to serve
                    your jbrowse instances, Apollo can serve public
                    jbrowse instances so you may not need to configure
                    jbrowse separately
                    <div><br>
                    </div>
                    <div><br>
                      <div>If you do want it separate, then we would
                        probably need to debug that error. If you have
                        the stack trace from the developer console, it
                        might narrow down exactly where the error comes
                        from. If the stack trace is minified and hard to
                        read, can possibly use a &quot;dev&quot; version of
                        jbrowse if it is too unreadable since it does
                        not minify the builds!
                        <div><br>
                        </div>
                        <div><br>
                        </div>
                        <div><br>
                        </div>
                        <div>-Colin</div>
                      </div>
                    </div>
                  </div>
                  <br>
                  <div class="gmail_quote">
                    <div dir="ltr" class="gmail_attr">On Wed, May 25,
                      2022 at 1:03 PM Justin Elser &lt;<a href="mailto:jus...@or..." rel="noreferrer noreferrer noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>&gt;
                      wrote:<br>
                    </div>
                    <blockquote class="gmail_quote" style="margin:0px
                      0px 0px 0.8ex;border-left:1px solid
                      rgb(204,204,204);padding-left:1ex">
                      <div>Yeah, so I guess the problem is that if I
                        don't add the &quot;dataset_id&quot; to each
                        data/(species)/tracks.conf file, apollo works
                        fine, but then I can't get the dataset selector
                        in jbrowse. As I have it right now, Apollo is
                        fine, but I have no way to switch to a different
                        dataset in JBrowse.<br>
                        <img src="cid:par...@or..." alt="" moz-do-not-send="true" width="1073" height="648"><br>
                        <br>
                        I was messing around with jbrowse.conf,
                        data/tracks.conf, and
                        data/(species)/tracks.conf, and was able to get
                        a list of the species under the &quot;Genome&quot; tab.
                        But if I don't have anything in
                        data/(species)/tracks.conf, I don't. However, if
                        I do add it like in the documentation, the
                        species are listed under there:<br>
                        <img src="cid:par...@or..." alt="" moz-do-not-send="true" width="1021" height="616"><br>
                        But then, apollo breaks:<br>
                        <img src="cid:par...@or..." alt="" moz-do-not-send="true" width="972" height="587"><br>
                        <br>
                        So, I guess I need to get the dataset_selector
                        working in JBrowse, while not breaking Apollo.<br>
                        <br>
                        I hope that clears it up more.<br>
                        <br>
                        Thanks,<br>
                        Justin<br>
                        <br>
                        <div>On 5/25/22 11:50 AM, Colin wrote:<br>
                        </div>
                        <blockquote type="cite">
                          <p><span style="color:rgb(215,63,9)">[This
                              email originated from outside of OSU. Use
                              caution with links and attachments.]</span></p>
                          <div>
                            <div dir="ltr">
                              <div>I haven't evaluated the whole post
                                here, but note that Apollo automatically
                                creates a dataset selector from
                                assemblies that you configure through
                                that Apollo interface</div>
                              <div><br>
                              </div>
                              <div>
                                <div><br>
                                </div>
                                <div>-Colin</div>
                              </div>
                            </div>
                            <br>
                            <div class="gmail_quote">
                              <div dir="ltr" class="gmail_attr">On Wed,
                                May 25, 2022 at 12:21 PM Justin Elser
                                &lt;<a href="mailto:jus...@or..." rel="noreferrer noreferrer noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>&gt;
                                wrote:<br>
                              </div>
                              <blockquote class="gmail_quote" style="margin:0px 0px 0px
                                0.8ex;border-left:1px solid
                                rgb(204,204,204);padding-left:1ex">
                                Hi all,<br>
                                <br>
                                I have set up a jbrowse 1.16.11 instance
                                (sorry, not publicly available) <br>
                                and added 2 species (well, different
                                cultivars) by doing the following:<br>
                                bin/<a href="http://prepare-refseqs.pl/" originalsrc="http://prepare-refseqs.pl/" shash="Iw7JIv8JSxSDakGiUb5b42Bd55gBvCt4+3TQJyt6NutlLU290Wx2IqOWIp5gDEiGUWJaCBDjpEfGozPb6ncagFq1AHUOlM7nQs4lIgTBhtQCE7h5xMQzIJoW92/4pX6pqzDclcxOWbatbmh27zPetOrxtomFvDrLnVinn1BiQF0=" rel="noreferrer noreferrer noreferrer
                                  noreferrer" title="Unmangled Microsoft
                                  Safelink" target="_blank" moz-do-not-send="true">prepare-refseqs.pl</a>
                                --out data/nipponbare --fasta
                                <br>
source_files/RAPDB-Reference-Nipponbare_chr_fixed.fasta<br>
                                bin/<a href="http://flatfile-to-json.pl/" originalsrc="http://flatfile-to-json.pl/" shash="djDv4cv/Q25cSdu8YcftqlGVE9DKJD0CIceloNveCO+o3AZubjfgaJteYEMhTJY1uT2bNR4NfoGYeM48i4H3LVQGHF1yzA/ZVnbYkSq1hDOP0V5p8yh9YYgREocd9Dm+n1MRZPQre0W+h3jISY+H+GyN2UQT/z362L6QsXdATX0=" rel="noreferrer noreferrer noreferrer
                                  noreferrer" title="Unmangled Microsoft
                                  Safelink" target="_blank" moz-do-not-send="true">flatfile-to-json.pl</a>
                                --out data/nipponbare --trackType
                                CanvasFeatures
                                <br>
                                --trackLabel MSU7.0 -gff
                                source_files/MSU7.0.gff3<br>
                                bin/<a href="http://generate-names.pl/" originalsrc="http://generate-names.pl/" shash="BozVmS4CdIphHrkpb9yb93YpWCD3ohMCi6uO2tznjLcnGqXfLhC2sjK6H+90f/pxP5+JjAPJbv48hEq0weXBVMj6Ptirgrof7VWV7y2r/G9gqFcjrO9HD4HzG3ZIG4aH4gnPv/3ji8eyWlbdLGbi/taDo6hyU+YFcHEC9XOjB4g=" rel="noreferrer noreferrer noreferrer
                                  noreferrer" title="Unmangled Microsoft
                                  Safelink" target="_blank" moz-do-not-send="true">generate-names.pl</a>
                                --out data/nipponbare<br>
                                <br>
                                bin/<a href="http://prepare-refseqs.pl/" originalsrc="http://prepare-refseqs.pl/" shash="Iw7JIv8JSxSDakGiUb5b42Bd55gBvCt4+3TQJyt6NutlLU290Wx2IqOWIp5gDEiGUWJaCBDjpEfGozPb6ncagFq1AHUOlM7nQs4lIgTBhtQCE7h5xMQzIJoW92/4pX6pqzDclcxOWbatbmh27zPetOrxtomFvDrLnVinn1BiQF0=" rel="noreferrer noreferrer noreferrer
                                  noreferrer" title="Unmangled Microsoft
                                  Safelink" target="_blank" moz-do-not-send="true">prepare-refseqs.pl</a>
                                --out data/arc --fasta
                                <br>
source_files/magic_16/oryza_sativa_arc.fa<br>
                                bin/<a href="http://flatfile-to-json.pl/" originalsrc="http://flatfile-to-json.pl/" shash="djDv4cv/Q25cSdu8YcftqlGVE9DKJD0CIceloNveCO+o3AZubjfgaJteYEMhTJY1uT2bNR4NfoGYeM48i4H3LVQGHF1yzA/ZVnbYkSq1hDOP0V5p8yh9YYgREocd9Dm+n1MRZPQre0W+h3jISY+H+GyN2UQT/z362L6QsXdATX0=" rel="noreferrer noreferrer noreferrer
                                  noreferrer" title="Unmangled Microsoft
                                  Safelink" target="_blank" moz-do-not-send="true">flatfile-to-json.pl</a>
                                --out data/arc --trackType
                                CanvasFeatures
                                <br>
                                --trackLabel Genes -gff
                                source_files/magic_16/oryza_sativa_arc.gff<br>
                                bin/<a href="http://generate-names.pl/" originalsrc="http://generate-names.pl/" shash="BozVmS4CdIphHrkpb9yb93YpWCD3ohMCi6uO2tznjLcnGqXfLhC2sjK6H+90f/pxP5+JjAPJbv48hEq0weXBVMj6Ptirgrof7VWV7y2r/G9gqFcjrO9HD4HzG3ZIG4aH4gnPv/3ji8eyWlbdLGbi/taDo6hyU+YFcHEC9XOjB4g=" rel="noreferrer noreferrer noreferrer
                                  noreferrer" title="Unmangled Microsoft
                                  Safelink" target="_blank" moz-do-not-send="true">generate-names.pl</a>
                                --out data/arc<br>
                                <br>
                                Then I edited the jbrowse.conf file as
                                explained in <br>
                                <a href="https://jbrowse.org/docs/dataset_selector.html" originalsrc="https://jbrowse.org/docs/dataset_selector.html" shash="I/Hc19jvjhytQo9VcQEUMphArpjSAzZBLWbP00xLK8q30977hYU+iIG5ukzKihOT6O6pqoYRHWBrKDzosuVSIzmA3fbT0Cru7PW/nHQpXYaltwuftgI7YChftu+aNs3y6RNiacz+6Zc+jKe8yXJ0Ddqetw+Ptuv7NsWIs6udSpY=" rel="noreferrer noreferrer noreferrer
                                  noreferrer" title="Unmangled Microsoft
                                  Safelink" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">https://jbrowse.org/docs/dataset_selector.html</a>
                                to have:<br>
                                dataRoot = data/nipponbare<br>
                                [datasets.nipponbare]<br>
                                url = ?data=data/nipponbare<br>
                                name = Nipponbare<br>
                                [datasets.arc]<br>
                                url = ?data=data/arc<br>
                                name = ARC<br>
                                <br>
                                And all seems to work fine, except that
                                I don't see the dropdown to <br>
                                switch datasets, so I can't actually see
                                the ARC dataset. Although I <br>
                                have by messing around with jbrowse.conf
                                and tracks.conf gotten it to <br>
                                work, but at this point I've left it
                                out.<br>
                                <br>
                                However, the issue I'm having is
                                actually with Apollo. I have the docker
                                <br>
                                instance of apollo running and it seems
                                to be fine as configured in a <br>
                                systemd unit file:<br>
                                ExecStart=/usr/bin/docker run --rm
                                --name %n \<br>
                                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -e APOLLO_PATH=apollo \<br>
                                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -v /data/www/panoryza/jbrowse/<a rel="noreferrer noreferrer noreferrer" moz-do-not-send="true">data:/data</a>
                                \<br>
                                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -v
                                /data/www/panoryza/apollo/postgres:/var/lib/postgresql
                                \<br>
                                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -v <br>
                                /data/www/panoryza/apollo/apollo_<a rel="noreferrer noreferrer noreferrer" moz-do-not-send="true">data:/data/temporary/apollo_data</a>
                                \<br>
                                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -p 8887:8080 \<br>
                                &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; gmod/apollo:latest<br>
                                <br>
                                Adding Nipponbare as an organism with
                                &quot;Directory&quot; /data/nipponbare works <br>
                                fine and I can see the tracks I've
                                added.<br>
                                <br>
                                Now, here is where the issue I have
                                starts. If I edit the <br>
                                data/nipponbare/tracks.conf file as
                                shown in the dataset selector <br>
                                documentation above:<br>
                                [general]<br>
                                dataset_id = nipponbare<br>
                                <br>
                                Apollo then shows the following error:<br>
                                Error message(s):<br>
                                &nbsp;&nbsp;&nbsp;&nbsp; TypeError: Cannot read properties
                                of undefined (reading 'name').<br>
                                <br>
                                Clearing out the
                                data/nipponbare/tracks.conf file allows
                                apollo to work.<br>
                                Now, the error only appears in apollo,
                                jbrowse works fine with the edits.<br>
                                <br>
                                I'm a bit confused about how this should
                                be configured to work. I <br>
                                actually have 14 more &quot;species&quot; to add,
                                but waiting till I at least get <br>
                                it working with one. The documentation
                                isn't clear to me on the <br>
                                difference between adding the datasets
                                to jbrowse.conf vs <br>
                                data/tracks.conf vs
                                data/(species)/tracks.conf.<br>
                                <br>
                                Please let me know if you need any more
                                information.<br>
                                <br>
                                Thanks,<br>
                                Justin<br>
                                <br>
                                -- <br>
**********************************************************<br>
                                *&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                                &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; *<br>
                                *&nbsp; Justin Elser&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                                &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; *<br>
                                *&nbsp; Computational Biology Research
                                Associate&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; *<br>
                                *&nbsp; Dept. of Botany and Plant Pathology&nbsp;
                                &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;*<br>
                                *&nbsp; Jaiswal Lab&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                                &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;*<br>
                                *&nbsp; Oregon State University&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                                &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;*<br>
                                *&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                                &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; *<br>
                                *&nbsp; email: <a href="mailto:jus...@or..." rel="noreferrer noreferrer noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">
                                  jus...@or...</a>&nbsp; &nbsp; &nbsp;
                                &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;*<br>
                                *&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                                &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; *<br>
**********************************************************<br>
                                <br>
                                <br>
                                <br>
_______________________________________________<br>
                                Gmod-ajax mailing list<br>
                                <a href="mailto:Gmo...@li..." rel="noreferrer noreferrer noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">Gmo...@li...</a><br>
                                <a href="https://lists.sourceforge.net/lists/listinfo/gmod-ajax" originalsrc="https://lists.sourceforge.net/lists/listinfo/gmod-ajax" shash="EPnrKpyvEtw7mAGHbeofol6OgROlyD2hqBp2Rvfgxo8sVXbT1DHMZzsuDOe+dVPgpobqDHHASWyoEnV2KXog53/ndTG1hwUjHk1BVJ94rKaUsnzLPBDzF0S5PloX/Tx8QTQSMo+fb3meY+KpcWlZuthmbavp2Gb/RU7gix9oosc=" rel="noreferrer noreferrer noreferrer
                                  noreferrer" title="Unmangled Microsoft
                                  Safelink" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">https://lists.sourceforge.net/lists/listinfo/gmod-ajax</a><br>
                              </blockquote>
                            </div>
                          </div>
                        </blockquote>
                        <br>
                        <pre cols="72">-- 
**********************************************************
*                                                        *
*  Justin Elser                                          *
*  Computational Biology Research Associate              *
*  Dept. of Botany and Plant Pathology                   *
*  Jaiswal Lab                                           *
*  Oregon State University                               *
*                                                        *
*  email: <a href="mailto:jus...@or..." rel="noreferrer noreferrer noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>                   *
*                                                        *
**********************************************************
</pre>
                      </div>
                    </blockquote>
                  </div>
                </div>
              </blockquote>
              <br>
              <pre cols="72">-- 
**********************************************************
*                                                        *
*  Justin Elser                                          *
*  Computational Biology Research Associate              *
*  Dept. of Botany and Plant Pathology                   *
*  Jaiswal Lab                                           *
*  Oregon State University                               *
*                                                        *
*  email: <a href="mailto:jus...@or..." rel="noreferrer noreferrer noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>                   *
*                                                        *
**********************************************************
</pre>
            </div>
          </blockquote>
        </div>
      </div>
    </blockquote>
    <br>
    <pre class="moz-signature" cols="72">-- 
**********************************************************
*                                                        *
*  Justin Elser                                          *
*  Computational Biology Research Associate              *
*  Dept. of Botany and Plant Pathology                   *
*  Jaiswal Lab                                           *
*  Oregon State University                               *
*                                                        *
*  email: <a class="moz-txt-link-abbreviated" href="mailto:jus...@or...">jus...@or...</a>                   *
*                                                        *
**********************************************************
</pre>
  </body>
</html>

Re: [Gmod-ajax] Dataset selector in apollo

[Justin E. <jus...@or...>]

<html><head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
  </head>
  <body>
    We may just use Apollo to serve both, but thought I might give it a
    try to see about JBrowse.<br>
    <br>
    I am attaching the output I get when I run the docker container with
    &quot;-e WEBAPOLLO_DEBUG=true&quot;.<br>
    <br>
    The blank lines are in between it working and not working. IE, lines
    1-483 are the initial startup and navigating to the site with Apollo
    working as expected. Lines 487 on are after changing
    data/nipponbare/tracks.conf to have:<br>
    [general]<br>
    dataset_id = nipponbare<br>
    <br>
    I do notice that after the change it is trying to open
/data/temporary/apollo_data/34-Nipponbare/sample_data/json/volvox/successfully_run
    (line 579) where it isn't before. I don't understand why it would be
    looking for the sample data at all. I never loaded it as a track or
    anything.<br>
    <br>
    I also notice for the initial load where it works that it is
    complaining about the mime_type for .bam files. I did alter the
    .htaccess for the jbrowse but not apollo, so I think those are
    fixable and unrelated. Weirdly enough, the bam track does load fine
    in Apollo where it didn't in JBrowse until I made the change to
    .htaccess.<br>
    <br>
    If you meant some other logs, please let me know how to get those
    and I will send them to you.<br>
    <br>
    Thanks,<br>
    Justin<br>
    <br>
    <div class="moz-cite-prefix">On 5/25/22 2:18 PM, Colin wrote:<br>
    </div>
    <blockquote type="cite" cite="mid:CA+...@ma...">
      
      <p><span style="color:#D73F09;">[This email originated from
          outside of OSU. Use caution with links and attachments.]</span></p>
      <div>
        <div dir="ltr">One option is to use Apollo to serve your jbrowse
          instances, Apollo can serve public jbrowse instances so you
          may not need to configure jbrowse separately
          <div><br>
          </div>
          <div><br>
            <div>If you do want it separate, then we would probably need
              to debug that error. If you have the stack trace from the
              developer console, it might narrow down exactly where the
              error comes from. If the stack trace is minified and hard
              to read, can possibly use a &quot;dev&quot; version of jbrowse if it
              is too unreadable since it does not minify the builds!
              <div><br>
              </div>
              <div><br>
              </div>
              <div><br>
              </div>
              <div>-Colin</div>
            </div>
          </div>
        </div>
        <br>
        <div class="gmail_quote">
          <div dir="ltr" class="gmail_attr">On Wed, May 25, 2022 at 1:03
            PM Justin Elser &lt;<a href="mailto:jus...@or..." moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>&gt;
            wrote:<br>
          </div>
          <blockquote class="gmail_quote" style="margin:0px 0px 0px
            0.8ex;border-left:1px solid
            rgb(204,204,204);padding-left:1ex">
            <div>Yeah, so I guess the problem is that if I don't add the
              &quot;dataset_id&quot; to each data/(species)/tracks.conf file,
              apollo works fine, but then I can't get the dataset
              selector in jbrowse. As I have it right now, Apollo is
              fine, but I have no way to switch to a different dataset
              in JBrowse.<br>
              <img src="cid:par...@or..." alt="" class="" width="1073" height="648"><br>
              <br>
              I was messing around with jbrowse.conf, data/tracks.conf,
              and data/(species)/tracks.conf, and was able to get a list
              of the species under the &quot;Genome&quot; tab. But if I don't have
              anything in data/(species)/tracks.conf, I don't. However,
              if I do add it like in the documentation, the species are
              listed under there:<br>
              <img src="cid:par...@or..." alt="" class="" width="1021" height="616"><br>
              But then, apollo breaks:<br>
              <img src="cid:par...@or..." alt="" class="" width="972" height="587"><br>
              <br>
              So, I guess I need to get the dataset_selector working in
              JBrowse, while not breaking Apollo.<br>
              <br>
              I hope that clears it up more.<br>
              <br>
              Thanks,<br>
              Justin<br>
              <br>
              <div>On 5/25/22 11:50 AM, Colin wrote:<br>
              </div>
              <blockquote type="cite">
                <p><span style="color:rgb(215,63,9)">[This email
                    originated from outside of OSU. Use caution with
                    links and attachments.]</span></p>
                <div>
                  <div dir="ltr">
                    <div>I haven't evaluated the whole post here, but
                      note that Apollo automatically creates a dataset
                      selector from assemblies that you configure
                      through that Apollo interface</div>
                    <div><br>
                    </div>
                    <div>
                      <div><br>
                      </div>
                      <div>-Colin</div>
                    </div>
                  </div>
                  <br>
                  <div class="gmail_quote">
                    <div dir="ltr" class="gmail_attr">On Wed, May 25,
                      2022 at 12:21 PM Justin Elser &lt;<a href="mailto:jus...@or..." target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>&gt;
                      wrote:<br>
                    </div>
                    <blockquote class="gmail_quote" style="margin:0px
                      0px 0px 0.8ex;border-left:1px solid
                      rgb(204,204,204);padding-left:1ex">
                      Hi all,<br>
                      <br>
                      I have set up a jbrowse 1.16.11 instance (sorry,
                      not publicly available) <br>
                      and added 2 species (well, different cultivars) by
                      doing the following:<br>
                      bin/<a href="http://prepare-refseqs.pl/" originalsrc="http://prepare-refseqs.pl/" shash="uWeJJjB9s93rzDNTEzCi3RakZCyt4ux/WC2ZoqKcYa1rGzS6R/h8TMuA3cBa8U1hWeK2PmNrobskt3PS6tzO83xSvYt7rTv1SbgQnAxOhm7gKfMpvabsYcnM1d34DS/QRKdyV+1JgHuKhc3KX5vyw/MDw8lj80BKnGa/HEkKbwk=" rel="noreferrer" title="Unmangled Microsoft
                        Safelink" target="_blank" moz-do-not-send="true">prepare-refseqs.pl</a>
                      --out data/nipponbare --fasta
                      <br>
source_files/RAPDB-Reference-Nipponbare_chr_fixed.fasta<br>
                      bin/<a href="http://flatfile-to-json.pl/" originalsrc="http://flatfile-to-json.pl/" shash="zKgfqQ8d6GV9SwADCBr1AuH+GzqREPTQ0IUT6KnLEGvLVN3OQBJEeXN0sj8J1BZ/Whw7CCTB3nzTFpFzurhKINO7cCc2gSnW6mGCwzlrajwbjAjJWd/Nr8u4TgNfCMXlUCvDU6DOUN35UhFScB531PcpYc1w/t/TMQVeRxqfc6w=" rel="noreferrer" title="Unmangled Microsoft
                        Safelink" target="_blank" moz-do-not-send="true">flatfile-to-json.pl</a>
                      --out data/nipponbare --trackType CanvasFeatures
                      <br>
                      --trackLabel MSU7.0 -gff source_files/MSU7.0.gff3<br>
                      bin/<a href="http://generate-names.pl/" originalsrc="http://generate-names.pl/" shash="AEsH1IjqM6NIi/IjuCY9OYb3R61LcMr+v40tJyq7GMpxdq0bFveddo2JRQoOUXs7Arkhb+jU9rw/xgeHNuAAw4ZfZrJ3WBIFKBNKLZcL6QtpeM16HJ8MOM9on5gPe7b3mewTLmJRcnUe+15HWEhZ+D5VCKN/MJfT80eVGKWeNYI=" rel="noreferrer" title="Unmangled Microsoft
                        Safelink" target="_blank" moz-do-not-send="true">generate-names.pl</a>
                      --out data/nipponbare<br>
                      <br>
                      bin/<a href="http://prepare-refseqs.pl/" originalsrc="http://prepare-refseqs.pl/" shash="uWeJJjB9s93rzDNTEzCi3RakZCyt4ux/WC2ZoqKcYa1rGzS6R/h8TMuA3cBa8U1hWeK2PmNrobskt3PS6tzO83xSvYt7rTv1SbgQnAxOhm7gKfMpvabsYcnM1d34DS/QRKdyV+1JgHuKhc3KX5vyw/MDw8lj80BKnGa/HEkKbwk=" rel="noreferrer" title="Unmangled Microsoft
                        Safelink" target="_blank" moz-do-not-send="true">prepare-refseqs.pl</a>
                      --out data/arc --fasta
                      <br>
                      source_files/magic_16/oryza_sativa_arc.fa<br>
                      bin/<a href="http://flatfile-to-json.pl/" originalsrc="http://flatfile-to-json.pl/" shash="zKgfqQ8d6GV9SwADCBr1AuH+GzqREPTQ0IUT6KnLEGvLVN3OQBJEeXN0sj8J1BZ/Whw7CCTB3nzTFpFzurhKINO7cCc2gSnW6mGCwzlrajwbjAjJWd/Nr8u4TgNfCMXlUCvDU6DOUN35UhFScB531PcpYc1w/t/TMQVeRxqfc6w=" rel="noreferrer" title="Unmangled Microsoft
                        Safelink" target="_blank" moz-do-not-send="true">flatfile-to-json.pl</a>
                      --out data/arc --trackType CanvasFeatures
                      <br>
                      --trackLabel Genes -gff
                      source_files/magic_16/oryza_sativa_arc.gff<br>
                      bin/<a href="http://generate-names.pl/" originalsrc="http://generate-names.pl/" shash="AEsH1IjqM6NIi/IjuCY9OYb3R61LcMr+v40tJyq7GMpxdq0bFveddo2JRQoOUXs7Arkhb+jU9rw/xgeHNuAAw4ZfZrJ3WBIFKBNKLZcL6QtpeM16HJ8MOM9on5gPe7b3mewTLmJRcnUe+15HWEhZ+D5VCKN/MJfT80eVGKWeNYI=" rel="noreferrer" title="Unmangled Microsoft
                        Safelink" target="_blank" moz-do-not-send="true">generate-names.pl</a>
                      --out data/arc<br>
                      <br>
                      Then I edited the jbrowse.conf file as explained
                      in <br>
                      <a href="https://jbrowse.org/docs/dataset_selector.html" originalsrc="https://jbrowse.org/docs/dataset_selector.html" shash="iTq9PpsQjfikWqhtGN7FCNRL57lgYKDKZzWc2TrzkiLKGUpqxn9A0TDQXbFwduJIfFcnzVaq3EPIiFw1fq504i6ZkF5ZYUVYuY4wX8IQ5vlk2nTXXBhYAbhx2olcMjrkYqC9+w9yTvpjRuewl+pJ9I5fMW5LUsH7pNqhziooqYs=" rel="noreferrer" title="Unmangled Microsoft
                        Safelink" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">https://jbrowse.org/docs/dataset_selector.html</a>
                      to have:<br>
                      dataRoot = data/nipponbare<br>
                      [datasets.nipponbare]<br>
                      url = ?data=data/nipponbare<br>
                      name = Nipponbare<br>
                      [datasets.arc]<br>
                      url = ?data=data/arc<br>
                      name = ARC<br>
                      <br>
                      And all seems to work fine, except that I don't
                      see the dropdown to <br>
                      switch datasets, so I can't actually see the ARC
                      dataset. Although I <br>
                      have by messing around with jbrowse.conf and
                      tracks.conf gotten it to <br>
                      work, but at this point I've left it out.<br>
                      <br>
                      However, the issue I'm having is actually with
                      Apollo. I have the docker <br>
                      instance of apollo running and it seems to be fine
                      as configured in a <br>
                      systemd unit file:<br>
                      ExecStart=/usr/bin/docker run --rm --name %n \<br>
                      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -e APOLLO_PATH=apollo \<br>
                      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -v /data/www/panoryza/jbrowse/<a moz-do-not-send="true">data:/data</a> \<br>
                      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -v
                      /data/www/panoryza/apollo/postgres:/var/lib/postgresql
                      \<br>
                      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -v <br>
                      /data/www/panoryza/apollo/apollo_<a moz-do-not-send="true">data:/data/temporary/apollo_data</a>
                      \<br>
                      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -p 8887:8080 \<br>
                      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; gmod/apollo:latest<br>
                      <br>
                      Adding Nipponbare as an organism with &quot;Directory&quot;
                      /data/nipponbare works <br>
                      fine and I can see the tracks I've added.<br>
                      <br>
                      Now, here is where the issue I have starts. If I
                      edit the <br>
                      data/nipponbare/tracks.conf file as shown in the
                      dataset selector <br>
                      documentation above:<br>
                      [general]<br>
                      dataset_id = nipponbare<br>
                      <br>
                      Apollo then shows the following error:<br>
                      Error message(s):<br>
                      &nbsp;&nbsp;&nbsp;&nbsp; TypeError: Cannot read properties of
                      undefined (reading 'name').<br>
                      <br>
                      Clearing out the data/nipponbare/tracks.conf file
                      allows apollo to work.<br>
                      Now, the error only appears in apollo, jbrowse
                      works fine with the edits.<br>
                      <br>
                      I'm a bit confused about how this should be
                      configured to work. I <br>
                      actually have 14 more &quot;species&quot; to add, but
                      waiting till I at least get <br>
                      it working with one. The documentation isn't clear
                      to me on the <br>
                      difference between adding the datasets to
                      jbrowse.conf vs <br>
                      data/tracks.conf vs data/(species)/tracks.conf.<br>
                      <br>
                      Please let me know if you need any more
                      information.<br>
                      <br>
                      Thanks,<br>
                      Justin<br>
                      <br>
                      -- <br>
**********************************************************<br>
                      *&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                      &nbsp; &nbsp; &nbsp; *<br>
                      *&nbsp; Justin Elser&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                      &nbsp; &nbsp; &nbsp; *<br>
                      *&nbsp; Computational Biology Research Associate&nbsp; &nbsp; &nbsp; &nbsp;
                      &nbsp; &nbsp; &nbsp; *<br>
                      *&nbsp; Dept. of Botany and Plant Pathology&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                      &nbsp; &nbsp; &nbsp; &nbsp;*<br>
                      *&nbsp; Jaiswal Lab&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                      &nbsp; &nbsp; &nbsp; &nbsp;*<br>
                      *&nbsp; Oregon State University&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                      &nbsp; &nbsp; &nbsp; &nbsp;*<br>
                      *&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                      &nbsp; &nbsp; &nbsp; *<br>
                      *&nbsp; email: <a href="mailto:jus...@or..." target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>&nbsp;
                      &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;*<br>
                      *&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
                      &nbsp; &nbsp; &nbsp; *<br>
**********************************************************<br>
                      <br>
                      <br>
                      <br>
                      _______________________________________________<br>
                      Gmod-ajax mailing list<br>
                      <a href="mailto:Gmo...@li..." target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">Gmo...@li...</a><br>
                      <a href="https://lists.sourceforge.net/lists/listinfo/gmod-ajax" originalsrc="https://lists.sourceforge.net/lists/listinfo/gmod-ajax" shash="NoO/SyLFO4FG/2TX9PVY+LlUUvQM7e/CR0zlDnnPXNXNaQiCZ661S1/SPNsdJeuUmcdnsF7NHbLg41Tg6tIppRE3SyniUabFDr7CXlTLiWF/jGYeZFUNdz7gYZ/pkTCUuJTxs4PD4vNj4JvEvqUqAWyP7frLtW02G/Y541kjFcA=" rel="noreferrer" title="Unmangled Microsoft
                        Safelink" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">https://lists.sourceforge.net/lists/listinfo/gmod-ajax</a><br>
                    </blockquote>
                  </div>
                </div>
              </blockquote>
              <br>
              <pre cols="72">-- 
**********************************************************
*                                                        *
*  Justin Elser                                          *
*  Computational Biology Research Associate              *
*  Dept. of Botany and Plant Pathology                   *
*  Jaiswal Lab                                           *
*  Oregon State University                               *
*                                                        *
*  email: <a href="mailto:jus...@or..." target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>                   *
*                                                        *
**********************************************************
</pre>
            </div>
          </blockquote>
        </div>
      </div>
    </blockquote>
    <br>
    <pre class="moz-signature" cols="72">-- 
**********************************************************
*                                                        *
*  Justin Elser                                          *
*  Computational Biology Research Associate              *
*  Dept. of Botany and Plant Pathology                   *
*  Jaiswal Lab                                           *
*  Oregon State University                               *
*                                                        *
*  email: <a class="moz-txt-link-abbreviated" href="mailto:jus...@or...">jus...@or...</a>                   *
*                                                        *
**********************************************************
</pre>
  </body>
</html>

Re: [Gmod-ajax] Dataset selector in apollo

[Colin <col...@gm...>]

The logs that are probably most helpful are the "JavaScript console" or
developer console from chrome or firefox e.g.
https://balsamiq.com/support/faqs/browserconsole/

On Wed, May 25, 2022, 4:33 PM Justin Elser <jus...@or...>
wrote:

> We may just use Apollo to serve both, but thought I might give it a try to
> see about JBrowse.
>
> I am attaching the output I get when I run the docker container with "-e
> WEBAPOLLO_DEBUG=true".
>
> The blank lines are in between it working and not working. IE, lines 1-483
> are the initial startup and navigating to the site with Apollo working as
> expected. Lines 487 on are after changing data/nipponbare/tracks.conf to
> have:
> [general]
> dataset_id = nipponbare
>
> I do notice that after the change it is trying to open
> /data/temporary/apollo_data/34-Nipponbare/sample_data/json/volvox/successfully_run
> (line 579) where it isn't before. I don't understand why it would be
> looking for the sample data at all. I never loaded it as a track or
> anything.
>
> I also notice for the initial load where it works that it is complaining
> about the mime_type for .bam files. I did alter the .htaccess for the
> jbrowse but not apollo, so I think those are fixable and unrelated. Weirdly
> enough, the bam track does load fine in Apollo where it didn't in JBrowse
> until I made the change to .htaccess.
>
> If you meant some other logs, please let me know how to get those and I
> will send them to you.
>
> Thanks,
> Justin
>
> On 5/25/22 2:18 PM, Colin wrote:
>
> [This email originated from outside of OSU. Use caution with links and
> attachments.]
> One option is to use Apollo to serve your jbrowse instances, Apollo can
> serve public jbrowse instances so you may not need to configure jbrowse
> separately
>
>
> If you do want it separate, then we would probably need to debug that
> error. If you have the stack trace from the developer console, it might
> narrow down exactly where the error comes from. If the stack trace is
> minified and hard to read, can possibly use a "dev" version of jbrowse if
> it is too unreadable since it does not minify the builds!
>
>
>
> -Colin
>
> On Wed, May 25, 2022 at 1:03 PM Justin Elser <jus...@or...>
> wrote:
>
>> Yeah, so I guess the problem is that if I don't add the "dataset_id" to
>> each data/(species)/tracks.conf file, apollo works fine, but then I can't
>> get the dataset selector in jbrowse. As I have it right now, Apollo is
>> fine, but I have no way to switch to a different dataset in JBrowse.
>>
>>
>> I was messing around with jbrowse.conf, data/tracks.conf, and
>> data/(species)/tracks.conf, and was able to get a list of the species under
>> the "Genome" tab. But if I don't have anything in
>> data/(species)/tracks.conf, I don't. However, if I do add it like in the
>> documentation, the species are listed under there:
>>
>> But then, apollo breaks:
>>
>>
>> So, I guess I need to get the dataset_selector working in JBrowse, while
>> not breaking Apollo.
>>
>> I hope that clears it up more.
>>
>> Thanks,
>> Justin
>>
>> On 5/25/22 11:50 AM, Colin wrote:
>>
>> [This email originated from outside of OSU. Use caution with links and
>> attachments.]
>> I haven't evaluated the whole post here, but note that Apollo
>> automatically creates a dataset selector from assemblies that you configure
>> through that Apollo interface
>>
>>
>> -Colin
>>
>> On Wed, May 25, 2022 at 12:21 PM Justin Elser <
>> jus...@or...> wrote:
>>
>>> Hi all,
>>>
>>> I have set up a jbrowse 1.16.11 instance (sorry, not publicly available)
>>> and added 2 species (well, different cultivars) by doing the following:
>>> bin/prepare-refseqs.pl --out data/nipponbare --fasta
>>> source_files/RAPDB-Reference-Nipponbare_chr_fixed.fasta
>>> bin/flatfile-to-json.pl --out data/nipponbare --trackType
>>> CanvasFeatures
>>> --trackLabel MSU7.0 -gff source_files/MSU7.0.gff3
>>> bin/generate-names.pl --out data/nipponbare
>>>
>>> bin/prepare-refseqs.pl --out data/arc --fasta
>>> source_files/magic_16/oryza_sativa_arc.fa
>>> bin/flatfile-to-json.pl --out data/arc --trackType CanvasFeatures
>>> --trackLabel Genes -gff source_files/magic_16/oryza_sativa_arc.gff
>>> bin/generate-names.pl --out data/arc
>>>
>>> Then I edited the jbrowse.conf file as explained in
>>> https://jbrowse.org/docs/dataset_selector.html to have:
>>> dataRoot = data/nipponbare
>>> [datasets.nipponbare]
>>> url = ?data=data/nipponbare
>>> name = Nipponbare
>>> [datasets.arc]
>>> url = ?data=data/arc
>>> name = ARC
>>>
>>> And all seems to work fine, except that I don't see the dropdown to
>>> switch datasets, so I can't actually see the ARC dataset. Although I
>>> have by messing around with jbrowse.conf and tracks.conf gotten it to
>>> work, but at this point I've left it out.
>>>
>>> However, the issue I'm having is actually with Apollo. I have the docker
>>> instance of apollo running and it seems to be fine as configured in a
>>> systemd unit file:
>>> ExecStart=/usr/bin/docker run --rm --name %n \
>>>          -e APOLLO_PATH=apollo \
>>>          -v /data/www/panoryza/jbrowse/data:/data \
>>>          -v /data/www/panoryza/apollo/postgres:/var/lib/postgresql \
>>>          -v
>>> /data/www/panoryza/apollo/apollo_data:/data/temporary/apollo_data \
>>>          -p 8887:8080 \
>>>          gmod/apollo:latest
>>>
>>> Adding Nipponbare as an organism with "Directory" /data/nipponbare works
>>> fine and I can see the tracks I've added.
>>>
>>> Now, here is where the issue I have starts. If I edit the
>>> data/nipponbare/tracks.conf file as shown in the dataset selector
>>> documentation above:
>>> [general]
>>> dataset_id = nipponbare
>>>
>>> Apollo then shows the following error:
>>> Error message(s):
>>>      TypeError: Cannot read properties of undefined (reading 'name').
>>>
>>> Clearing out the data/nipponbare/tracks.conf file allows apollo to work.
>>> Now, the error only appears in apollo, jbrowse works fine with the edits.
>>>
>>> I'm a bit confused about how this should be configured to work. I
>>> actually have 14 more "species" to add, but waiting till I at least get
>>> it working with one. The documentation isn't clear to me on the
>>> difference between adding the datasets to jbrowse.conf vs
>>> data/tracks.conf vs data/(species)/tracks.conf.
>>>
>>> Please let me know if you need any more information.
>>>
>>> Thanks,
>>> Justin
>>>
>>> --
>>> **********************************************************
>>> *                                                        *
>>> *  Justin Elser                                          *
>>> *  Computational Biology Research Associate              *
>>> *  Dept. of Botany and Plant Pathology                   *
>>> *  Jaiswal Lab                                           *
>>> *  Oregon State University                               *
>>> *                                                        *
>>> *  email: jus...@or...                   *
>>> *                                                        *
>>> **********************************************************
>>>
>>>
>>>
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>
>> --
>> **********************************************************
>> *                                                        *
>> *  Justin Elser                                          *
>> *  Computational Biology Research Associate              *
>> *  Dept. of Botany and Plant Pathology                   *
>> *  Jaiswal Lab                                           *
>> *  Oregon State University                               *
>> *                                                        *
>> *  email: jus...@or...                   *
>> *                                                        *
>> **********************************************************
>>
>>
> --
> **********************************************************
> *                                                        *
> *  Justin Elser                                          *
> *  Computational Biology Research Associate              *
> *  Dept. of Botany and Plant Pathology                   *
> *  Jaiswal Lab                                           *
> *  Oregon State University                               *
> *                                                        *
> *  email: jus...@or...                   *
> *                                                        *
> **********************************************************
>
>

Re: [Gmod-ajax] Dataset selector in apollo

[Colin <col...@gm...>]

One option is to use Apollo to serve your jbrowse instances, Apollo can
serve public jbrowse instances so you may not need to configure jbrowse
separately


If you do want it separate, then we would probably need to debug that
error. If you have the stack trace from the developer console, it might
narrow down exactly where the error comes from. If the stack trace is
minified and hard to read, can possibly use a "dev" version of jbrowse if
it is too unreadable since it does not minify the builds!



-Colin

On Wed, May 25, 2022 at 1:03 PM Justin Elser <jus...@or...>
wrote:

> Yeah, so I guess the problem is that if I don't add the "dataset_id" to
> each data/(species)/tracks.conf file, apollo works fine, but then I can't
> get the dataset selector in jbrowse. As I have it right now, Apollo is
> fine, but I have no way to switch to a different dataset in JBrowse.
>
>
> I was messing around with jbrowse.conf, data/tracks.conf, and
> data/(species)/tracks.conf, and was able to get a list of the species under
> the "Genome" tab. But if I don't have anything in
> data/(species)/tracks.conf, I don't. However, if I do add it like in the
> documentation, the species are listed under there:
>
> But then, apollo breaks:
>
>
> So, I guess I need to get the dataset_selector working in JBrowse, while
> not breaking Apollo.
>
> I hope that clears it up more.
>
> Thanks,
> Justin
>
> On 5/25/22 11:50 AM, Colin wrote:
>
> [This email originated from outside of OSU. Use caution with links and
> attachments.]
> I haven't evaluated the whole post here, but note that Apollo
> automatically creates a dataset selector from assemblies that you configure
> through that Apollo interface
>
>
> -Colin
>
> On Wed, May 25, 2022 at 12:21 PM Justin Elser <
> jus...@or...> wrote:
>
>> Hi all,
>>
>> I have set up a jbrowse 1.16.11 instance (sorry, not publicly available)
>> and added 2 species (well, different cultivars) by doing the following:
>> bin/prepare-refseqs.pl --out data/nipponbare --fasta
>> source_files/RAPDB-Reference-Nipponbare_chr_fixed.fasta
>> bin/flatfile-to-json.pl --out data/nipponbare --trackType CanvasFeatures
>> --trackLabel MSU7.0 -gff source_files/MSU7.0.gff3
>> bin/generate-names.pl --out data/nipponbare
>>
>> bin/prepare-refseqs.pl --out data/arc --fasta
>> source_files/magic_16/oryza_sativa_arc.fa
>> bin/flatfile-to-json.pl --out data/arc --trackType CanvasFeatures
>> --trackLabel Genes -gff source_files/magic_16/oryza_sativa_arc.gff
>> bin/generate-names.pl --out data/arc
>>
>> Then I edited the jbrowse.conf file as explained in
>> https://jbrowse.org/docs/dataset_selector.html to have:
>> dataRoot = data/nipponbare
>> [datasets.nipponbare]
>> url = ?data=data/nipponbare
>> name = Nipponbare
>> [datasets.arc]
>> url = ?data=data/arc
>> name = ARC
>>
>> And all seems to work fine, except that I don't see the dropdown to
>> switch datasets, so I can't actually see the ARC dataset. Although I
>> have by messing around with jbrowse.conf and tracks.conf gotten it to
>> work, but at this point I've left it out.
>>
>> However, the issue I'm having is actually with Apollo. I have the docker
>> instance of apollo running and it seems to be fine as configured in a
>> systemd unit file:
>> ExecStart=/usr/bin/docker run --rm --name %n \
>>          -e APOLLO_PATH=apollo \
>>          -v /data/www/panoryza/jbrowse/data:/data \
>>          -v /data/www/panoryza/apollo/postgres:/var/lib/postgresql \
>>          -v
>> /data/www/panoryza/apollo/apollo_data:/data/temporary/apollo_data \
>>          -p 8887:8080 \
>>          gmod/apollo:latest
>>
>> Adding Nipponbare as an organism with "Directory" /data/nipponbare works
>> fine and I can see the tracks I've added.
>>
>> Now, here is where the issue I have starts. If I edit the
>> data/nipponbare/tracks.conf file as shown in the dataset selector
>> documentation above:
>> [general]
>> dataset_id = nipponbare
>>
>> Apollo then shows the following error:
>> Error message(s):
>>      TypeError: Cannot read properties of undefined (reading 'name').
>>
>> Clearing out the data/nipponbare/tracks.conf file allows apollo to work.
>> Now, the error only appears in apollo, jbrowse works fine with the edits.
>>
>> I'm a bit confused about how this should be configured to work. I
>> actually have 14 more "species" to add, but waiting till I at least get
>> it working with one. The documentation isn't clear to me on the
>> difference between adding the datasets to jbrowse.conf vs
>> data/tracks.conf vs data/(species)/tracks.conf.
>>
>> Please let me know if you need any more information.
>>
>> Thanks,
>> Justin
>>
>> --
>> **********************************************************
>> *                                                        *
>> *  Justin Elser                                          *
>> *  Computational Biology Research Associate              *
>> *  Dept. of Botany and Plant Pathology                   *
>> *  Jaiswal Lab                                           *
>> *  Oregon State University                               *
>> *                                                        *
>> *  email: jus...@or...                   *
>> *                                                        *
>> **********************************************************
>>
>>
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
> --
> **********************************************************
> *                                                        *
> *  Justin Elser                                          *
> *  Computational Biology Research Associate              *
> *  Dept. of Botany and Plant Pathology                   *
> *  Jaiswal Lab                                           *
> *  Oregon State University                               *
> *                                                        *
> *  email: jus...@or...                   *
> *                                                        *
> **********************************************************
>
>

Re: [Gmod-ajax] Dataset selector in apollo

[Justin E. <jus...@or...>]

<html><head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
  </head>
  <body>
    Yeah, so I guess the problem is that if I don't add the &quot;dataset_id&quot;
    to each data/(species)/tracks.conf file, apollo works fine, but then
    I can't get the dataset selector in jbrowse. As I have it right now,
    Apollo is fine, but I have no way to switch to a different dataset
    in JBrowse.<br>
    <img src="cid:par...@or..." alt="" width="1073" height="648"><br>
    <br>
    I was messing around with jbrowse.conf, data/tracks.conf, and
    data/(species)/tracks.conf, and was able to get a list of the
    species under the &quot;Genome&quot; tab. But if I don't have anything in
    data/(species)/tracks.conf, I don't. However, if I do add it like in
    the documentation, the species are listed under there:<br>
    <img src="cid:par...@or..." alt="" width="1021" height="616"><br>
    But then, apollo breaks:<br>
    <img src="cid:par...@or..." alt="" width="972" height="587"><br>
    <br>
    So, I guess I need to get the dataset_selector working in JBrowse,
    while not breaking Apollo.<br>
    <br>
    I hope that clears it up more.<br>
    <br>
    Thanks,<br>
    Justin<br>
    <br>
    <div class="moz-cite-prefix">On 5/25/22 11:50 AM, Colin wrote:<br>
    </div>
    <blockquote type="cite" cite="mid:CA+ZENa+MSWvYgomL84twRKSKyrV+0unVAWpdwOaFGQ+=2k...@ma...">
      
      <p><span style="color:#D73F09;">[This email originated from
          outside of OSU. Use caution with links and attachments.]</span></p>
      <div>
        <div dir="ltr">
          <div>I haven't evaluated the whole post here, but note that
            Apollo automatically creates a dataset selector from
            assemblies that you configure through that Apollo interface</div>
          <div><br>
          </div>
          <div>
            <div><br>
            </div>
            <div>-Colin</div>
          </div>
        </div>
        <br>
        <div class="gmail_quote">
          <div dir="ltr" class="gmail_attr">On Wed, May 25, 2022 at
            12:21 PM Justin Elser &lt;<a href="mailto:jus...@or..." moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>&gt;
            wrote:<br>
          </div>
          <blockquote class="gmail_quote" style="margin:0px 0px 0px
            0.8ex;border-left:1px solid
            rgb(204,204,204);padding-left:1ex">
            Hi all,<br>
            <br>
            I have set up a jbrowse 1.16.11 instance (sorry, not
            publicly available) <br>
            and added 2 species (well, different cultivars) by doing the
            following:<br>
            bin/<a href="http://prepare-refseqs.pl/" originalsrc="http://prepare-refseqs.pl/" shash="vDZg07JxIpNJ9SgJzz2LwjbWbu8SZAiokVgcdDRj6LUgO6iAMhYwW9Z0FIXdB5UtpFCd8QZr6rEERKDxgPH2e0Ce9zF2mnoTCJR7X9AdyU5lhWNpvjgxOdixxU6R4+74IQmdEOmb04yVM89miQnoEc/JygeEmooSw18QFFvfdW4=" rel="noreferrer" target="_blank" moz-do-not-send="true" title="Unmangled Microsoft Safelink">prepare-refseqs.pl</a>
            --out data/nipponbare --fasta
            <br>
            source_files/RAPDB-Reference-Nipponbare_chr_fixed.fasta<br>
            bin/<a href="http://flatfile-to-json.pl/" originalsrc="http://flatfile-to-json.pl/" shash="jz4oaK2Wo/C+nxugXiV44jGiRLNVPLRJfJryV/FsZWPhUZV+IYb1pvz92/AWbU+u3PUDNN8/G/N6Cwm8enn0OYBQn6cpy8WqsLts/2aWjxm3+bLCz+9iF5tayFpWacmHXEi4xH8rwGZHYdSh0fHbCWVzgB70NW+yXrS9gcUpn7Y=" rel="noreferrer" target="_blank" moz-do-not-send="true" title="Unmangled Microsoft Safelink">flatfile-to-json.pl</a>
            --out data/nipponbare --trackType CanvasFeatures
            <br>
            --trackLabel MSU7.0 -gff source_files/MSU7.0.gff3<br>
            bin/<a href="http://generate-names.pl/" originalsrc="http://generate-names.pl/" shash="TsXMi6c3CubeCT8PiCe0pyMle3yjX2ZziNDXE4nXnX8sfBIiqA5ma1QZSf0NeGul85lIAyVU30OuJs2bcs8NjeHw56utqne7+ELMoWBQTUF9zcdEyN3nuqvReN7OyvazMClcqtPxIjZBGEegA8Psod2d2hYxjJ8WuQVlHB57LyY=" rel="noreferrer" target="_blank" moz-do-not-send="true" title="Unmangled Microsoft Safelink">generate-names.pl</a>
            --out data/nipponbare<br>
            <br>
            bin/<a href="http://prepare-refseqs.pl/" originalsrc="http://prepare-refseqs.pl/" shash="vDZg07JxIpNJ9SgJzz2LwjbWbu8SZAiokVgcdDRj6LUgO6iAMhYwW9Z0FIXdB5UtpFCd8QZr6rEERKDxgPH2e0Ce9zF2mnoTCJR7X9AdyU5lhWNpvjgxOdixxU6R4+74IQmdEOmb04yVM89miQnoEc/JygeEmooSw18QFFvfdW4=" rel="noreferrer" target="_blank" moz-do-not-send="true" title="Unmangled Microsoft Safelink">prepare-refseqs.pl</a>
            --out data/arc --fasta
            <br>
            source_files/magic_16/oryza_sativa_arc.fa<br>
            bin/<a href="http://flatfile-to-json.pl/" originalsrc="http://flatfile-to-json.pl/" shash="vWccfMWLvZwkIbe4x7F6sdOJGPKKVxaaBtExf9G4aS8kXEwkgZczQ42oy341GccmCCj6fg7IVTE3tz+bX+jeKzhnCEO0rwD1nMpBGz5Jvxl/xSy3ZlE4ddlZ89plKxnGIsfo2jWC8EmcL3sJgGNLU7SqC6ZyDi4R4uR6yIY8ub0=" rel="noreferrer" target="_blank" moz-do-not-send="true" title="Unmangled Microsoft Safelink">flatfile-to-json.pl</a>
            --out data/arc --trackType CanvasFeatures
            <br>
            --trackLabel Genes -gff
            source_files/magic_16/oryza_sativa_arc.gff<br>
            bin/<a href="http://generate-names.pl/" originalsrc="http://generate-names.pl/" shash="lH56QhD00nWxUgDDOxKhXeL6CA6BS+gRwqKHZgDCdToe1e+3Vdeo81Iv9fNyjQFecc/d1WQ994kfGApGN89fCDMnx/eghC4t1s6pYzvAp0HfCouryb6mB45fL3s+GmhVhm5Vf0CDxGlMZQGcpezRYayo9e6B0jJBiNR0Pc/HOaY=" rel="noreferrer" target="_blank" moz-do-not-send="true" title="Unmangled Microsoft Safelink">generate-names.pl</a>
            --out data/arc<br>
            <br>
            Then I edited the jbrowse.conf file as explained in <br>
            <a href="https://jbrowse.org/docs/dataset_selector.html" originalsrc="https://jbrowse.org/docs/dataset_selector.html" shash="TNt2K6nKz3VtRTClTdZhLEyShTUc4ZraZlvMeeMoUF8lUY6IdV/F//7+nviwFOXfPTwjlXcpU9jenaatyJynMD285YAxD5658VNkwcK8UzugOvxgQ6KyKl1VOOdGFspTk2W4KK5svCk7clykEtDbRFwJy9Lin2+zmc0vaiRSByI=" rel="noreferrer" target="_blank" moz-do-not-send="true" title="Unmangled Microsoft Safelink" class="moz-txt-link-freetext">https://jbrowse.org/docs/dataset_selector.html</a>
            to have:<br>
            dataRoot = data/nipponbare<br>
            [datasets.nipponbare]<br>
            url = ?data=data/nipponbare<br>
            name = Nipponbare<br>
            [datasets.arc]<br>
            url = ?data=data/arc<br>
            name = ARC<br>
            <br>
            And all seems to work fine, except that I don't see the
            dropdown to <br>
            switch datasets, so I can't actually see the ARC dataset.
            Although I <br>
            have by messing around with jbrowse.conf and tracks.conf
            gotten it to <br>
            work, but at this point I've left it out.<br>
            <br>
            However, the issue I'm having is actually with Apollo. I
            have the docker <br>
            instance of apollo running and it seems to be fine as
            configured in a <br>
            systemd unit file:<br>
            ExecStart=/usr/bin/docker run --rm --name %n \<br>
            &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -e APOLLO_PATH=apollo \<br>
            &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -v /data/www/panoryza/jbrowse/<a class="moz-txt-link-freetext" href="data:/data">data:/data</a> \<br>
            &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -v
            /data/www/panoryza/apollo/postgres:/var/lib/postgresql \<br>
            &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -v <br>
/data/www/panoryza/apollo/apollo_<a class="moz-txt-link-freetext" href="data:/data/temporary/apollo_data">data:/data/temporary/apollo_data</a> \<br>
            &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -p 8887:8080 \<br>
            &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; gmod/apollo:latest<br>
            <br>
            Adding Nipponbare as an organism with &quot;Directory&quot;
            /data/nipponbare works <br>
            fine and I can see the tracks I've added.<br>
            <br>
            Now, here is where the issue I have starts. If I edit the <br>
            data/nipponbare/tracks.conf file as shown in the dataset
            selector <br>
            documentation above:<br>
            [general]<br>
            dataset_id = nipponbare<br>
            <br>
            Apollo then shows the following error:<br>
            Error message(s):<br>
            &nbsp;&nbsp;&nbsp;&nbsp; TypeError: Cannot read properties of undefined (reading
            'name').<br>
            <br>
            Clearing out the data/nipponbare/tracks.conf file allows
            apollo to work.<br>
            Now, the error only appears in apollo, jbrowse works fine
            with the edits.<br>
            <br>
            I'm a bit confused about how this should be configured to
            work. I <br>
            actually have 14 more &quot;species&quot; to add, but waiting till I
            at least get <br>
            it working with one. The documentation isn't clear to me on
            the <br>
            difference between adding the datasets to jbrowse.conf vs <br>
            data/tracks.conf vs data/(species)/tracks.conf.<br>
            <br>
            Please let me know if you need any more information.<br>
            <br>
            Thanks,<br>
            Justin<br>
            <br>
            -- <br>
            **********************************************************<br>
            *&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; *<br>
            *&nbsp; Justin Elser&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; *<br>
            *&nbsp; Computational Biology Research Associate&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; *<br>
            *&nbsp; Dept. of Botany and Plant Pathology&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;*<br>
            *&nbsp; Jaiswal Lab&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;*<br>
            *&nbsp; Oregon State University&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;*<br>
            *&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; *<br>
            *&nbsp; email: <a href="mailto:jus...@or..." target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">jus...@or...</a>&nbsp;
            &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;*<br>
            *&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; *<br>
            **********************************************************<br>
            <br>
            <br>
            <br>
            _______________________________________________<br>
            Gmod-ajax mailing list<br>
            <a href="mailto:Gmo...@li..." target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">Gmo...@li...</a><br>
            <a href="https://lists.sourceforge.net/lists/listinfo/gmod-ajax" originalsrc="https://lists.sourceforge.net/lists/listinfo/gmod-ajax" shash="GbwbWEy14gGDziZJSrKQhQTAWjCJGyUG5PhtseEVugNFLO7L/k5oeGae4eFUHCbsFXhMt9VQPGHQLR+hWGekfUHsewAHeSHxu1CfvmCUE8szi2i+Yo/SdeFrCdTw2t2Iu+FXXWp20BNo0MJR44jsp1YtLdt2CeeOWk6Vt2GXEgM=" rel="noreferrer" target="_blank" moz-do-not-send="true" title="Unmangled Microsoft Safelink" class="moz-txt-link-freetext">https://lists.sourceforge.net/lists/listinfo/gmod-ajax</a><br>
          </blockquote>
        </div>
      </div>
    </blockquote>
    <br>
    <pre class="moz-signature" cols="72">-- 
**********************************************************
*                                                        *
*  Justin Elser                                          *
*  Computational Biology Research Associate              *
*  Dept. of Botany and Plant Pathology                   *
*  Jaiswal Lab                                           *
*  Oregon State University                               *
*                                                        *
*  email: <a class="moz-txt-link-abbreviated" href="mailto:jus...@or...">jus...@or...</a>                   *
*                                                        *
**********************************************************
</pre>
  </body>
</html>

Re: [Gmod-ajax] Dataset selector in apollo

[Colin <col...@gm...>]

I haven't evaluated the whole post here, but note that Apollo automatically
creates a dataset selector from assemblies that you configure through that
Apollo interface


-Colin

On Wed, May 25, 2022 at 12:21 PM Justin Elser <jus...@or...>
wrote:

> Hi all,
>
> I have set up a jbrowse 1.16.11 instance (sorry, not publicly available)
> and added 2 species (well, different cultivars) by doing the following:
> bin/prepare-refseqs.pl --out data/nipponbare --fasta
> source_files/RAPDB-Reference-Nipponbare_chr_fixed.fasta
> bin/flatfile-to-json.pl --out data/nipponbare --trackType CanvasFeatures
> --trackLabel MSU7.0 -gff source_files/MSU7.0.gff3
> bin/generate-names.pl --out data/nipponbare
>
> bin/prepare-refseqs.pl --out data/arc --fasta
> source_files/magic_16/oryza_sativa_arc.fa
> bin/flatfile-to-json.pl --out data/arc --trackType CanvasFeatures
> --trackLabel Genes -gff source_files/magic_16/oryza_sativa_arc.gff
> bin/generate-names.pl --out data/arc
>
> Then I edited the jbrowse.conf file as explained in
> https://jbrowse.org/docs/dataset_selector.html to have:
> dataRoot = data/nipponbare
> [datasets.nipponbare]
> url = ?data=data/nipponbare
> name = Nipponbare
> [datasets.arc]
> url = ?data=data/arc
> name = ARC
>
> And all seems to work fine, except that I don't see the dropdown to
> switch datasets, so I can't actually see the ARC dataset. Although I
> have by messing around with jbrowse.conf and tracks.conf gotten it to
> work, but at this point I've left it out.
>
> However, the issue I'm having is actually with Apollo. I have the docker
> instance of apollo running and it seems to be fine as configured in a
> systemd unit file:
> ExecStart=/usr/bin/docker run --rm --name %n \
>          -e APOLLO_PATH=apollo \
>          -v /data/www/panoryza/jbrowse/data:/data \
>          -v /data/www/panoryza/apollo/postgres:/var/lib/postgresql \
>          -v
> /data/www/panoryza/apollo/apollo_data:/data/temporary/apollo_data \
>          -p 8887:8080 \
>          gmod/apollo:latest
>
> Adding Nipponbare as an organism with "Directory" /data/nipponbare works
> fine and I can see the tracks I've added.
>
> Now, here is where the issue I have starts. If I edit the
> data/nipponbare/tracks.conf file as shown in the dataset selector
> documentation above:
> [general]
> dataset_id = nipponbare
>
> Apollo then shows the following error:
> Error message(s):
>      TypeError: Cannot read properties of undefined (reading 'name').
>
> Clearing out the data/nipponbare/tracks.conf file allows apollo to work.
> Now, the error only appears in apollo, jbrowse works fine with the edits.
>
> I'm a bit confused about how this should be configured to work. I
> actually have 14 more "species" to add, but waiting till I at least get
> it working with one. The documentation isn't clear to me on the
> difference between adding the datasets to jbrowse.conf vs
> data/tracks.conf vs data/(species)/tracks.conf.
>
> Please let me know if you need any more information.
>
> Thanks,
> Justin
>
> --
> **********************************************************
> *                                                        *
> *  Justin Elser                                          *
> *  Computational Biology Research Associate              *
> *  Dept. of Botany and Plant Pathology                   *
> *  Jaiswal Lab                                           *
> *  Oregon State University                               *
> *                                                        *
> *  email: jus...@or...                   *
> *                                                        *
> **********************************************************
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] Dataset selector in apollo

[Justin E. <jus...@or...>]

Hi all,

I have set up a jbrowse 1.16.11 instance (sorry, not publicly available) 
and added 2 species (well, different cultivars) by doing the following:
bin/prepare-refseqs.pl --out data/nipponbare --fasta 
source_files/RAPDB-Reference-Nipponbare_chr_fixed.fasta
bin/flatfile-to-json.pl --out data/nipponbare --trackType CanvasFeatures 
--trackLabel MSU7.0 -gff source_files/MSU7.0.gff3
bin/generate-names.pl --out data/nipponbare

bin/prepare-refseqs.pl --out data/arc --fasta 
source_files/magic_16/oryza_sativa_arc.fa
bin/flatfile-to-json.pl --out data/arc --trackType CanvasFeatures 
--trackLabel Genes -gff source_files/magic_16/oryza_sativa_arc.gff
bin/generate-names.pl --out data/arc

Then I edited the jbrowse.conf file as explained in 
https://jbrowse.org/docs/dataset_selector.html to have:
dataRoot = data/nipponbare
[datasets.nipponbare]
url = ?data=data/nipponbare
name = Nipponbare
[datasets.arc]
url = ?data=data/arc
name = ARC

And all seems to work fine, except that I don't see the dropdown to 
switch datasets, so I can't actually see the ARC dataset. Although I 
have by messing around with jbrowse.conf and tracks.conf gotten it to 
work, but at this point I've left it out.

However, the issue I'm having is actually with Apollo. I have the docker 
instance of apollo running and it seems to be fine as configured in a 
systemd unit file:
ExecStart=/usr/bin/docker run --rm --name %n \
         -e APOLLO_PATH=apollo \
         -v /data/www/panoryza/jbrowse/data:/data \
         -v /data/www/panoryza/apollo/postgres:/var/lib/postgresql \
         -v 
/data/www/panoryza/apollo/apollo_data:/data/temporary/apollo_data \
         -p 8887:8080 \
         gmod/apollo:latest

Adding Nipponbare as an organism with "Directory" /data/nipponbare works 
fine and I can see the tracks I've added.

Now, here is where the issue I have starts. If I edit the 
data/nipponbare/tracks.conf file as shown in the dataset selector 
documentation above:
[general]
dataset_id = nipponbare

Apollo then shows the following error:
Error message(s):
     TypeError: Cannot read properties of undefined (reading 'name').

Clearing out the data/nipponbare/tracks.conf file allows apollo to work.
Now, the error only appears in apollo, jbrowse works fine with the edits.

I'm a bit confused about how this should be configured to work. I 
actually have 14 more "species" to add, but waiting till I at least get 
it working with one. The documentation isn't clear to me on the 
difference between adding the datasets to jbrowse.conf vs 
data/tracks.conf vs data/(species)/tracks.conf.

Please let me know if you need any more information.

Thanks,
Justin

-- 
**********************************************************
*                                                        *
*  Justin Elser                                          *
*  Computational Biology Research Associate              *
*  Dept. of Botany and Plant Pathology                   *
*  Jaiswal Lab                                           *
*  Oregon State University                               *
*                                                        *
*  email: jus...@or...                   *
*                                                        *
**********************************************************

Re: [Gmod-ajax] [External] Re: Inquiry

[Colin <col...@gm...>]

Hi there

>Where can i find the webserver Jbower with mm10 genome

We have the fasta file for mm10 online as indicated in your screenshot but
the gene track/gff is not online currently. You can use the steps from the
gist I posted to add it locally to your desktop instance

Hope that helps

-Colin

On Mon, May 23, 2022 at 5:06 PM Chang, Hsi <xz...@iu...> wrote:

> Thanks, I use the desktop version.
>
> Where can i find the webserver Jbower with mm10 genome
>
>
> ------------------------------
> *From:* Scott Cain <sc...@sc...>
> *Sent:* Monday, May 23, 2022 2:12 PM
> *To:* Chang, Hsi <xz...@iu...>; gmod-ajax <gmo...@li...
> >
> *Subject:* Re: [External] Re: [Gmod-ajax] Inquiry
>
> You don't often get email from sc...@sc.... Learn why this is
> important <https://aka.ms/LearnAboutSenderIdentification>
> Please keep the JBrowse mailing list looped in, since more eyes==more
> chance of finding the problem!
>
> Is this in the desktop application or the webserved JBrowse? Can you send
> a jbrowse.conf file (which you would have if it's a web application)?
> Troubleshooting the desktop application might be a little harder, but I
> imagine there is a problem configuring the search index. If you're using
> the desktop version, can you send a screenshot of the configuration window
> around configuring search for the mouse genome?
>
> On Mon, May 23, 2022 at 10:55 AM Chang, Hsi <xz...@iu...> wrote:
>
> I test on my laptop.  Yes, i am not able to put a gene name into the box
> instead only coordinate.
>  No problem when using the human genome.
>
>
> ------------------------------
> *From:* Scott Cain <sc...@sc...>
> *Sent:* Monday, May 23, 2022 1:36 PM
> *To:* Chang, Hsi <xz...@iu...>
> *Cc:* gmo...@li... <gmo...@li...>
> *Subject:* [External] Re: [Gmod-ajax] Inquiry
>
> You don't often get email from sc...@sc.... Learn why this is
> important <https://aka.ms/LearnAboutSenderIdentification>
> This message was sent from a non-IU address. Please exercise caution when
> clicking links or opening attachments from external sources.
>
> Hi,
>
> Can you give us a little more information? Is this in a publicly available
> JBrowse instance? Can you give us a URL? When you write "Select the
> region", are you searching for something and it isn't working?
>
> Thanks,
> Scott
>
>
> On Mon, May 23, 2022 at 10:25 AM Chang, Hsi <xz...@iu...> wrote:
>
> I don't know I am not available select the region based on the gene for
> mm10 genome, but the hg38 working fine.
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
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> Scott Cain, Ph. D.                                                  scott
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> Scott Cain, Ph. D.                                                  scott
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Re: [Gmod-ajax] [External] Re: Inquiry

[Colin <col...@gm...>]

GRCm39 referred to from that link would not match mm10
GRCm38 is mm10

You could use https://www.gencodegenes.org/mouse/release_M25.html on mm10,
since it is GRCm38

Alternatively, you could load the GRCm39 (aka mm39
https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/) fasta file

And then, yes, to load the GFF file, you go through similar steps, using gt
gff3 -sortlines+bgzip+tabix and then add it as a track


-Colin


On Mon, May 23, 2022 at 2:24 PM Chang, Hsi <xz...@iu...> wrote:

> can i use the gff3 file from here
> https://www.gencodegenes.org/mouse/release_M29.html
> GENCODE - Mouse Release M29
> <https://www.gencodegenes.org/mouse/release_M29.html>
> Content Regions Description Download; Comprehensive gene annotation: CHR:
> It contains the comprehensive gene annotation on the reference chromosomes
> only
> www.gencodegenes.org
>
> ------------------------------
> *From:* Chang, Hsi <xz...@iu...>
> *Sent:* Monday, May 23, 2022 4:22 PM
> *To:* Colin <col...@gm...>
> *Subject:* Re: [Gmod-ajax] [External] Re: Inquiry
>
> Thanks, here is the error i got:
>
> brew install cufflinks
>
> Warning: No available formula with the name "cufflinks".
>
> ==> *Searching for similarly named formulae...*
>
> Error: No similarly named formulae found.
>
> ==> *Searching for a previously deleted formula (in the last month)...*
>
> Error: No previously deleted formula found.
>
> ==> *Searching taps on GitHub...*
>
> ------------------------------
> *From:* Colin <col...@gm...>
> *Sent:* Monday, May 23, 2022 4:06 PM
> *To:* Chang, Hsi <xz...@iu...>
> *Cc:* Scott Cain <sc...@sc...>; gmod-ajax <
> gmo...@li...>
> *Subject:* Re: [Gmod-ajax] [External] Re: Inquiry
>
> You don't often get email from col...@gm.... Learn why this is
> important <https://aka.ms/LearnAboutSenderIdentification>
> I made a short document to show how you can create a searchable gene track
> on mm10, starting from a UCSC gtf file. I convert it to a GFF3Tabix file
> and then go through the "Add track" widget in JBrowse Desktop making sure
> to add the gene_name field for indexing (see screenshots)
>
> https://gist.github.com/cmdcolin/30f3842c559c80253c3e7c250f94a7b5
> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgist.github.com%2Fcmdcolin%2F30f3842c559c80253c3e7c250f94a7b5&data=05%7C01%7Cxz87%40iu.edu%7Cd299baab42964a1cbba208da3cf7e1f4%7C1113be34aed14d00ab4bcdd02510be91%7C0%7C0%7C637889333487378485%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000%7C%7C%7C&sdata=%2BP8q6RDAM5uPm4Da7cJE48FXlFu0a%2BIj5DfrLqaGD98%3D&reserved=0>
>
> -Colin
>
> On Mon, May 23, 2022 at 1:21 PM Chang, Hsi <xz...@iu...> wrote:
>
> is there a way i can add a gene track?  or on the webserver?
> ------------------------------
> *From:* Colin <col...@gm...>
> *Sent:* Monday, May 23, 2022 3:15 PM
> *To:* Scott Cain <sc...@sc...>
> *Cc:* Chang, Hsi <xz...@iu...>; gmod-ajax <gmo...@li...
> >
> *Subject:* Re: [Gmod-ajax] [External] Re: Inquiry
>
> You don't often get email from col...@gm.... Learn why this is
> important <https://aka.ms/LearnAboutSenderIdentification>
> Thanks for reporting, Mm10 is a default genome that we ship in JBrowse 2
> desktop, but we have not fleshed it out as a resource and it does not yet
> have a gene track or gene names indexed
>
>
> We can definitely add this to our todo list!
>
>
>
> -Colin
>
> On Mon, May 23, 2022 at 12:18 PM Scott Cain <sc...@sc...> wrote:
>
> Please keep the JBrowse mailing list looped in, since more eyes==more
> chance of finding the problem!
>
> Is this in the desktop application or the webserved JBrowse? Can you send
> a jbrowse.conf file (which you would have if it's a web application)?
> Troubleshooting the desktop application might be a little harder, but I
> imagine there is a problem configuring the search index. If you're using
> the desktop version, can you send a screenshot of the configuration window
> around configuring search for the mouse genome?
>
> On Mon, May 23, 2022 at 10:55 AM Chang, Hsi <xz...@iu...> wrote:
>
> I test on my laptop.  Yes, i am not able to put a gene name into the box
> instead only coordinate.
>  No problem when using the human genome.
>
>
> ------------------------------
> *From:* Scott Cain <sc...@sc...>
> *Sent:* Monday, May 23, 2022 1:36 PM
> *To:* Chang, Hsi <xz...@iu...>
> *Cc:* gmo...@li... <gmo...@li...>
> *Subject:* [External] Re: [Gmod-ajax] Inquiry
>
> You don't often get email from sc...@sc.... Learn why this is
> important <https://aka.ms/LearnAboutSenderIdentification>
> This message was sent from a non-IU address. Please exercise caution when
> clicking links or opening attachments from external sources.
>
> Hi,
>
> Can you give us a little more information? Is this in a publicly available
> JBrowse instance? Can you give us a URL? When you write "Select the
> region", are you searching for something and it isn't working?
>
> Thanks,
> Scott
>
>
> On Mon, May 23, 2022 at 10:25 AM Chang, Hsi <xz...@iu...> wrote:
>
> I don't know I am not available select the region based on the gene for
> mm10 genome, but the hg38 working fine.
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> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                                  scott
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> Scott Cain, Ph. D.                                                  scott
> at scottcain dot net
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Re: [Gmod-ajax] [External] Re: Inquiry

[Colin <col...@gm...>]

I made a short document to show how you can create a searchable gene track
on mm10, starting from a UCSC gtf file. I convert it to a GFF3Tabix file
and then go through the "Add track" widget in JBrowse Desktop making sure
to add the gene_name field for indexing (see screenshots)

https://gist.github.com/cmdcolin/30f3842c559c80253c3e7c250f94a7b5

-Colin

On Mon, May 23, 2022 at 1:21 PM Chang, Hsi <xz...@iu...> wrote:

> is there a way i can add a gene track?  or on the webserver?
> ------------------------------
> *From:* Colin <col...@gm...>
> *Sent:* Monday, May 23, 2022 3:15 PM
> *To:* Scott Cain <sc...@sc...>
> *Cc:* Chang, Hsi <xz...@iu...>; gmod-ajax <gmo...@li...
> >
> *Subject:* Re: [Gmod-ajax] [External] Re: Inquiry
>
> You don't often get email from col...@gm.... Learn why this is
> important <https://aka.ms/LearnAboutSenderIdentification>
> Thanks for reporting, Mm10 is a default genome that we ship in JBrowse 2
> desktop, but we have not fleshed it out as a resource and it does not yet
> have a gene track or gene names indexed
>
>
> We can definitely add this to our todo list!
>
>
>
> -Colin
>
> On Mon, May 23, 2022 at 12:18 PM Scott Cain <sc...@sc...> wrote:
>
> Please keep the JBrowse mailing list looped in, since more eyes==more
> chance of finding the problem!
>
> Is this in the desktop application or the webserved JBrowse? Can you send
> a jbrowse.conf file (which you would have if it's a web application)?
> Troubleshooting the desktop application might be a little harder, but I
> imagine there is a problem configuring the search index. If you're using
> the desktop version, can you send a screenshot of the configuration window
> around configuring search for the mouse genome?
>
> On Mon, May 23, 2022 at 10:55 AM Chang, Hsi <xz...@iu...> wrote:
>
> I test on my laptop.  Yes, i am not able to put a gene name into the box
> instead only coordinate.
>  No problem when using the human genome.
>
>
> ------------------------------
> *From:* Scott Cain <sc...@sc...>
> *Sent:* Monday, May 23, 2022 1:36 PM
> *To:* Chang, Hsi <xz...@iu...>
> *Cc:* gmo...@li... <gmo...@li...>
> *Subject:* [External] Re: [Gmod-ajax] Inquiry
>
> You don't often get email from sc...@sc.... Learn why this is
> important <https://aka.ms/LearnAboutSenderIdentification>
> This message was sent from a non-IU address. Please exercise caution when
> clicking links or opening attachments from external sources.
>
> Hi,
>
> Can you give us a little more information? Is this in a publicly available
> JBrowse instance? Can you give us a URL? When you write "Select the
> region", are you searching for something and it isn't working?
>
> Thanks,
> Scott
>
>
> On Mon, May 23, 2022 at 10:25 AM Chang, Hsi <xz...@iu...> wrote:
>
> I don't know I am not available select the region based on the gene for
> mm10 genome, but the hg38 working fine.
> _______________________________________________
> Gmod-ajax mailing list
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> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
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>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                                  scott
> at scottcain dot net
> GMOD Project Manager (http://gmod.org/
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>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                                  scott
> at scottcain dot net
> GMOD Project Manager (http://gmod.org/
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>                           216-392-3087
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> )
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>
>

Re: [Gmod-ajax] [External] Re: Inquiry

[Chang, H. <xz...@iu...>]

is there a way i can add a gene track?  or on the webserver?
________________________________
From: Colin <col...@gm...>
Sent: Monday, May 23, 2022 3:15 PM
To: Scott Cain <sc...@sc...>
Cc: Chang, Hsi <xz...@iu...>; gmod-ajax <gmo...@li...>
Subject: Re: [Gmod-ajax] [External] Re: Inquiry

You don't often get email from col...@gm.... Learn why this is important<https://aka.ms/LearnAboutSenderIdentification>
Thanks for reporting, Mm10 is a default genome that we ship in JBrowse 2 desktop, but we have not fleshed it out as a resource and it does not yet have a gene track or gene names indexed


We can definitely add this to our todo list!



-Colin

On Mon, May 23, 2022 at 12:18 PM Scott Cain <sc...@sc...<mailto:sc...@sc...>> wrote:
Please keep the JBrowse mailing list looped in, since more eyes==more chance of finding the problem!

Is this in the desktop application or the webserved JBrowse? Can you send a jbrowse.conf file (which you would have if it's a web application)? Troubleshooting the desktop application might be a little harder, but I imagine there is a problem configuring the search index. If you're using the desktop version, can you send a screenshot of the configuration window around configuring search for the mouse genome?

On Mon, May 23, 2022 at 10:55 AM Chang, Hsi <xz...@iu...<mailto:xz...@iu...>> wrote:
I test on my laptop.  Yes, i am not able to put a gene name into the box instead only coordinate.
 No problem when using the human genome.

[cid:180f21ae87dcb971f161]
________________________________
From: Scott Cain <sc...@sc...<mailto:sc...@sc...>>
Sent: Monday, May 23, 2022 1:36 PM
To: Chang, Hsi <xz...@iu...<mailto:xz...@iu...>>
Cc: gmo...@li...<mailto:gmo...@li...> <gmo...@li...<mailto:gmo...@li...>>
Subject: [External] Re: [Gmod-ajax] Inquiry

You don't often get email from sc...@sc...<mailto:sc...@sc...>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification>
This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources.

Hi,

Can you give us a little more information? Is this in a publicly available JBrowse instance? Can you give us a URL? When you write "Select the region", are you searching for something and it isn't working?

Thanks,
Scott


On Mon, May 23, 2022 at 10:25 AM Chang, Hsi <xz...@iu...<mailto:xz...@iu...>> wrote:
I don't know I am not available select the region based on the gene for mm10 genome, but the hg38 working fine.
_______________________________________________
Gmod-ajax mailing list
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Scott Cain, Ph. D.                                                  scott at scottcain dot net
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Human Cancer Models Initiative Project Manager (https://hcmi-searchable-catalog.nci.nih.gov/<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhcmi-searchable-catalog.nci.nih.gov%2F&data=05%7C01%7Cxz87%40iu.edu%7Cf4c95224dde34f0be11e08da3cf0a3e0%7C1113be34aed14d00ab4bcdd02510be91%7C0%7C0%7C637889302073596271%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000%7C%7C%7C&sdata=lzjwovfba2bAUAGpHxQSkG6zGRZhyfNf%2BxjTpg%2FuKfE%3D&reserved=0>)
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Re: [Gmod-ajax] [External] Re: Inquiry

[Colin <col...@gm...>]

Thanks for reporting, Mm10 is a default genome that we ship in JBrowse 2
desktop, but we have not fleshed it out as a resource and it does not yet
have a gene track or gene names indexed


We can definitely add this to our todo list!



-Colin

On Mon, May 23, 2022 at 12:18 PM Scott Cain <sc...@sc...> wrote:

> Please keep the JBrowse mailing list looped in, since more eyes==more
> chance of finding the problem!
>
> Is this in the desktop application or the webserved JBrowse? Can you send
> a jbrowse.conf file (which you would have if it's a web application)?
> Troubleshooting the desktop application might be a little harder, but I
> imagine there is a problem configuring the search index. If you're using
> the desktop version, can you send a screenshot of the configuration window
> around configuring search for the mouse genome?
>
> On Mon, May 23, 2022 at 10:55 AM Chang, Hsi <xz...@iu...> wrote:
>
>> I test on my laptop.  Yes, i am not able to put a gene name into the box
>> instead only coordinate.
>>  No problem when using the human genome.
>>
>>
>> ------------------------------
>> *From:* Scott Cain <sc...@sc...>
>> *Sent:* Monday, May 23, 2022 1:36 PM
>> *To:* Chang, Hsi <xz...@iu...>
>> *Cc:* gmo...@li... <gmo...@li...>
>> *Subject:* [External] Re: [Gmod-ajax] Inquiry
>>
>> You don't often get email from sc...@sc.... Learn why this is
>> important <https://aka.ms/LearnAboutSenderIdentification>
>> This message was sent from a non-IU address. Please exercise caution when
>> clicking links or opening attachments from external sources.
>>
>> Hi,
>>
>> Can you give us a little more information? Is this in a publicly
>> available JBrowse instance? Can you give us a URL? When you write "Select
>> the region", are you searching for something and it isn't working?
>>
>> Thanks,
>> Scott
>>
>>
>> On Mon, May 23, 2022 at 10:25 AM Chang, Hsi <xz...@iu...> wrote:
>>
>> I don't know I am not available select the region based on the gene for
>> mm10 genome, but the hg38 working fine.
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fgmod-ajax&data=05%7C01%7Cxz87%40iu.edu%7Ca348cfe0e25548dc8cf508da3ce2e047%7C1113be34aed14d00ab4bcdd02510be91%7C0%7C0%7C637889242368767405%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Bq%2Fwh73pfSEYBt29cXIR%2FppkANRsJiZFbCuV98s1AYU%3D&reserved=0>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                                  scott
>> at scottcain dot net
>> GMOD Project Manager (http://gmod.org/
>> <https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgmod.org%2F&data=05%7C01%7Cxz87%40iu.edu%7Ca348cfe0e25548dc8cf508da3ce2e047%7C1113be34aed14d00ab4bcdd02510be91%7C0%7C0%7C637889242368767405%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=TGrhbM9qtF1qANq%2F9jQ7juSMrJKjFWwelG1Vcb%2F8%2BtI%3D&reserved=0>)
>>                           216-392-3087
>> WormBase Developer (http://wormbase.org/
>> <https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwormbase.org%2F&data=05%7C01%7Cxz87%40iu.edu%7Ca348cfe0e25548dc8cf508da3ce2e047%7C1113be34aed14d00ab4bcdd02510be91%7C0%7C0%7C637889242368767405%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=pC2HWkICiEhNwc9Vl7%2BSZ7N3JfLnrgR%2BbMTwsc5d6gQ%3D&reserved=0>
>> )
>> Alliance of Genome Resources Group Leader (http://alliancegenome.org/
>> <https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Falliancegenome.org%2F&data=05%7C01%7Cxz87%40iu.edu%7Ca348cfe0e25548dc8cf508da3ce2e047%7C1113be34aed14d00ab4bcdd02510be91%7C0%7C0%7C637889242368767405%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Ioi6znKFbZr7CPoHJlS%2BcaeX19PLfQBrZ37KAa08Hmk%3D&reserved=0>
>> )
>> VirusSeq Project Manager (https://virusseq-dataportal.ca/
>> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fvirusseq-dataportal.ca%2F&data=05%7C01%7Cxz87%40iu.edu%7Ca348cfe0e25548dc8cf508da3ce2e047%7C1113be34aed14d00ab4bcdd02510be91%7C0%7C0%7C637889242368767405%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=CeX5FLeaGH0Z9dqgyKPNdMTbANKQLAYYAQy6axbN5cU%3D&reserved=0>
>> )
>> Human Cancer Models Initiative Project Manager (
>> https://hcmi-searchable-catalog.nci.nih.gov/
>> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhcmi-searchable-catalog.nci.nih.gov%2F&data=05%7C01%7Cxz87%40iu.edu%7Ca348cfe0e25548dc8cf508da3ce2e047%7C1113be34aed14d00ab4bcdd02510be91%7C0%7C0%7C637889242368767405%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=3x3PoXwVkWvCg3nGaSHSRSaEH82%2BiM3Ph4Q7DuIORms%3D&reserved=0>
>> )
>>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                                  scott
> at scottcain dot net
> GMOD Project Manager (http://gmod.org/)
> 216-392-3087
> WormBase Developer (http://wormbase.org/)
> Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
> VirusSeq Project Manager (https://virusseq-dataportal.ca/)
> Human Cancer Models Initiative Project Manager (
> https://hcmi-searchable-catalog.nci.nih.gov/)
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] [External] Re: Inquiry

[Chang, H. <xz...@iu...>]

Thanks, I use the desktop version.

Where can i find the webserver Jbower with mm10 genome

[cid:4d942090-286e-4d5d-a33f-cbdae4623ce9]
________________________________
From: Scott Cain <sc...@sc...>
Sent: Monday, May 23, 2022 2:12 PM
To: Chang, Hsi <xz...@iu...>; gmod-ajax <gmo...@li...>
Subject: Re: [External] Re: [Gmod-ajax] Inquiry

You don't often get email from sc...@sc.... Learn why this is important<https://aka.ms/LearnAboutSenderIdentification>
Please keep the JBrowse mailing list looped in, since more eyes==more chance of finding the problem!

Is this in the desktop application or the webserved JBrowse? Can you send a jbrowse.conf file (which you would have if it's a web application)? Troubleshooting the desktop application might be a little harder, but I imagine there is a problem configuring the search index. If you're using the desktop version, can you send a screenshot of the configuration window around configuring search for the mouse genome?

On Mon, May 23, 2022 at 10:55 AM Chang, Hsi <xz...@iu...<mailto:xz...@iu...>> wrote:
I test on my laptop.  Yes, i am not able to put a gene name into the box instead only coordinate.
 No problem when using the human genome.

[cid:180f21ae87dcb971f161]
________________________________
From: Scott Cain <sc...@sc...<mailto:sc...@sc...>>
Sent: Monday, May 23, 2022 1:36 PM
To: Chang, Hsi <xz...@iu...<mailto:xz...@iu...>>
Cc: gmo...@li...<mailto:gmo...@li...> <gmo...@li...<mailto:gmo...@li...>>
Subject: [External] Re: [Gmod-ajax] Inquiry

You don't often get email from sc...@sc...<mailto:sc...@sc...>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification>
This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources.

Hi,

Can you give us a little more information? Is this in a publicly available JBrowse instance? Can you give us a URL? When you write "Select the region", are you searching for something and it isn't working?

Thanks,
Scott


On Mon, May 23, 2022 at 10:25 AM Chang, Hsi <xz...@iu...<mailto:xz...@iu...>> wrote:
I don't know I am not available select the region based on the gene for mm10 genome, but the hg38 working fine.
_______________________________________________
Gmod-ajax mailing list
Gmo...@li...<mailto:Gmo...@li...>
https://lists.sourceforge.net/lists/listinfo/gmod-ajax<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fgmod-ajax&data=05%7C01%7Cxz87%40iu.edu%7C14961a44afc142f205b208da3ce7d1f1%7C1113be34aed14d00ab4bcdd02510be91%7C0%7C0%7C637889263600337351%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=sYo1WeTZVvB7NnVBDkpFOKeKM2o0TqNlvr0226bCHZI%3D&reserved=0>


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                                  scott at scottcain dot net
GMOD Project Manager (http://gmod.org/<https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgmod.org%2F&data=05%7C01%7Cxz87%40iu.edu%7C14961a44afc142f205b208da3ce7d1f1%7C1113be34aed14d00ab4bcdd02510be91%7C0%7C0%7C637889263600337351%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=oyGNPsjQxSNeEwRsfI1j9KcG7B2L0JAmpPnbRocZhKM%3D&reserved=0>)                            216-392-3087
WormBase Developer (http://wormbase.org/<https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwormbase.org%2F&data=05%7C01%7Cxz87%40iu.edu%7C14961a44afc142f205b208da3ce7d1f1%7C1113be34aed14d00ab4bcdd02510be91%7C0%7C0%7C637889263600493587%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=AbvmE9sHjhpd9K%2FYx7D9lJRS3eVR%2BWmwqq4dqxG9EXU%3D&reserved=0>)
Alliance of Genome Resources Group Leader (http://alliancegenome.org/<https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Falliancegenome.org%2F&data=05%7C01%7Cxz87%40iu.edu%7C14961a44afc142f205b208da3ce7d1f1%7C1113be34aed14d00ab4bcdd02510be91%7C0%7C0%7C637889263600493587%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Lfjq6UW0PLDqZL6dWn34cX5AE7aTETFny4%2FkXypSGK4%3D&reserved=0>)
VirusSeq Project Manager (https://virusseq-dataportal.ca/<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fvirusseq-dataportal.ca%2F&data=05%7C01%7Cxz87%40iu.edu%7C14961a44afc142f205b208da3ce7d1f1%7C1113be34aed14d00ab4bcdd02510be91%7C0%7C0%7C637889263600493587%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=j%2BHnjZaAqYcXHCCyYnw7aChcY3vS8028pUjoA2YbLxY%3D&reserved=0>)
Human Cancer Models Initiative Project Manager (https://hcmi-searchable-catalog.nci.nih.gov/<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhcmi-searchable-catalog.nci.nih.gov%2F&data=05%7C01%7Cxz87%40iu.edu%7C14961a44afc142f205b208da3ce7d1f1%7C1113be34aed14d00ab4bcdd02510be91%7C0%7C0%7C637889263600493587%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=5EzKCKNT126Ea2TmIabXg1%2BjUXCiucUopgDWdl7f2%2FQ%3D&reserved=0>)


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                                  scott at scottcain dot net
GMOD Project Manager (http://gmod.org/<https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgmod.org%2F&data=05%7C01%7Cxz87%40iu.edu%7C14961a44afc142f205b208da3ce7d1f1%7C1113be34aed14d00ab4bcdd02510be91%7C0%7C0%7C637889263600493587%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=aBYS17Vl5kFksEg0ioqZr6oQrtCwvyBWsK3RJSvejmw%3D&reserved=0>)                            216-392-3087
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Re: [Gmod-ajax] [External] Re: Inquiry

[Scott C. <sc...@sc...>]

Please keep the JBrowse mailing list looped in, since more eyes==more
chance of finding the problem!

Is this in the desktop application or the webserved JBrowse? Can you send a
jbrowse.conf file (which you would have if it's a web application)?
Troubleshooting the desktop application might be a little harder, but I
imagine there is a problem configuring the search index. If you're using
the desktop version, can you send a screenshot of the configuration window
around configuring search for the mouse genome?

On Mon, May 23, 2022 at 10:55 AM Chang, Hsi <xz...@iu...> wrote:

> I test on my laptop.  Yes, i am not able to put a gene name into the box
> instead only coordinate.
>  No problem when using the human genome.
>
>
> ------------------------------
> *From:* Scott Cain <sc...@sc...>
> *Sent:* Monday, May 23, 2022 1:36 PM
> *To:* Chang, Hsi <xz...@iu...>
> *Cc:* gmo...@li... <gmo...@li...>
> *Subject:* [External] Re: [Gmod-ajax] Inquiry
>
> You don't often get email from sc...@sc.... Learn why this is
> important <https://aka.ms/LearnAboutSenderIdentification>
> This message was sent from a non-IU address. Please exercise caution when
> clicking links or opening attachments from external sources.
>
> Hi,
>
> Can you give us a little more information? Is this in a publicly available
> JBrowse instance? Can you give us a URL? When you write "Select the
> region", are you searching for something and it isn't working?
>
> Thanks,
> Scott
>
>
> On Mon, May 23, 2022 at 10:25 AM Chang, Hsi <xz...@iu...> wrote:
>
> I don't know I am not available select the region based on the gene for
> mm10 genome, but the hg38 working fine.
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fgmod-ajax&data=05%7C01%7Cxz87%40iu.edu%7Ca348cfe0e25548dc8cf508da3ce2e047%7C1113be34aed14d00ab4bcdd02510be91%7C0%7C0%7C637889242368767405%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Bq%2Fwh73pfSEYBt29cXIR%2FppkANRsJiZFbCuV98s1AYU%3D&reserved=0>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                                  scott
> at scottcain dot net
> GMOD Project Manager (http://gmod.org/
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                                  scott
at scottcain dot net
GMOD Project Manager (http://gmod.org/)
216-392-3087
WormBase Developer (http://wormbase.org/)
Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
VirusSeq Project Manager (https://virusseq-dataportal.ca/)
Human Cancer Models Initiative Project Manager (
https://hcmi-searchable-catalog.nci.nih.gov/)

Re: [Gmod-ajax] Inquiry

[Scott C. <sc...@sc...>]

Hi,

Can you give us a little more information? Is this in a publicly available
JBrowse instance? Can you give us a URL? When you write "Select the
region", are you searching for something and it isn't working?

Thanks,
Scott


On Mon, May 23, 2022 at 10:25 AM Chang, Hsi <xz...@iu...> wrote:

> I don't know I am not available select the region based on the gene for
> mm10 genome, but the hg38 working fine.
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                                  scott
at scottcain dot net
GMOD Project Manager (http://gmod.org/)
216-392-3087
WormBase Developer (http://wormbase.org/)
Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
VirusSeq Project Manager (https://virusseq-dataportal.ca/)
Human Cancer Models Initiative Project Manager (
https://hcmi-searchable-catalog.nci.nih.gov/)

[Gmod-ajax] Inquiry

[Chang, H. <xz...@iu...>]

I don't know I am not available select the region based on the gene for mm10 genome, but the hg38 working fine.