gmod-ajax — JBrowse list

Re: [Gmod-ajax] hic track on jb2 [EXT]

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

With the BED file, it is likely a similar thing: JBrowse expects the names
to exactly match, even the capitalization. You can standardize this or
alternatively configure refNameAliases. refNameAliases allows different
names to be interpreted as coming from the same source

See
https://jbrowse.org/jb2/docs/config_guide/#configuring-reference-name-aliasing
for example

-Colin

On Fri, May 20, 2022 at 9:59 AM Ying Sims <yy...@sa...> wrote:

> Hi Colin,
>
>
>
> Thanks for getting back to me.
>
>
>
> I am sorry the content has repeatedly shown in differently places, I
> wasn’t sure where to get immediate help. As addressed in the previous
> email, JB2 would highly likely used as gEVAL replace, it would become an
> essential tools in Darwin tree of life, I am eagerly making it fully
> functionable.
>
>
>
> It would be great that bionano plugin is available soon, it would make
> huge convenience to our genome evaluation work. Please let me know anything
> we could do at our ends.
>
>
>
> I have another question regarding bed file track. Similar issue as it
> doesn’t show on the browser. The bed file is in gz together with tbi, the
> content is as below:
>
> scaffold_1           233421 233621
>
> scaffold_1           275958 276158
>
> scaffold_1           891914 892114
>
> scaffold_1           3507111               3507311
>
> scaffold_1           5410752               5410952
>
>
>
> I wonder if the name of scaffold has to be capitals?
>
>
>
>
>
> Kindest
>
> Yumi
>
>
>
> *From: *Colin <col...@gm...>
> *Date: *Thursday, 19 May 2022 at 19:31
> *To: *Ying Sims <yy...@sa...>
> *Cc: *"gmo...@li..." <gmo...@li...>
> *Subject: *Re: [Gmod-ajax] hic track on jb2 [EXT]
>
>
>
> Hi Ying,
>
> I think some of this dialog is continued in various other places
> (github/gitter) but to answer
>
>
>
>
>
> 1) JBrowse 1 plugins will not work with JBrowse 2 unfortunately, but as
> you have done, a request for support is here https://github.com/GMOD/jbrowse-components/issues/2962
> [github.com]
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_GMOD_jbrowse-2Dcomponents_issues_2962&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=X9VPYUGy4ibZarh9Rup1XaZ62i2u-I0xOZXEy11dXDM&m=2h4i5rjVAcMUOLuJG5ET8RL8r1px37m0nkj5yAy1VdKoa8DBqDWo4DqgwkuPfpJp&s=VE2KzZVtvhWMDUrKzKZ4pJZpopf4Gt2dThdSQ5fbUgw&e=>
> :)
>
> 2) I think you said that this was resolved, now, by making the scaffold
> names match the FASTA, but let us know if you have any other concerns
>
>
>
>
>
> -Colin
>
>
>
> On Thu, May 19, 2022 at 9:44 AM Ying Sims <yy...@sa...> wrote:
>
> Hello,
>
>
>
> I am a bioinformatician works on the Darwin Tree of life project in Sanger
> institute (https://www.darwintreeoflife.org/). I am currently
> investigating jbrowse2 functionality, and think it could potentially
> replace our dated genome curation platform(gEVAL).  I have a couple of
> questions/problem would like to have your help.
>
>
>
>    1. I noticed bionano plugin is available, I also noticed the plugin
>    was developed in 2016, would it work in jb2?
>    2. I use jbrowse cli to load the tracks and assembly. Assembly fasta
>    loads fine,  but bed files and hic files are problematic for me. The hic
>    track doesn't show at all. I have changed the scaffold name in the fasta to
>    capitals but still nothing showed. The following is the command I used to
>    load the hic file. The hic can be displayed in juicebox as I have checked.
>
> *jbrowse add-track ~/data/bPtePen1_1/bPtePen1_1_arima.hic -l symlink -a
> bPtePen1_1*
>
>
>
> *and in the json: *
>
> *"tracks": [*
>
> *    {*
>
> *      "type": "HicTrack",*
>
> *      "trackId": "bPtePen1_1_arima",*
>
> *      "name": "bPtePen1_1_arima",*
>
> *      "adapter": {*
>
> *        "type": "HicAdapter",*
>
> *        "hicLocation": {*
>
> *          "uri": "bPtePen1_1_arima.hic",*
>
> *          "locationType": "UriLocation"*
>
> *        }*
>
> *      },*
>
> *      "assemblyNames": [*
>
> *        "bPtePen1_1"*
>
> *      ]*
>
>
>
> Could you please help
>
>
>
>
>
> Kind regards
>
> Yumi
>
> -- The Wellcome Sanger Institute is operated by Genome Research Limited, a
> charity registered in England with number 1021457 and a company registered
> in England with number 2742969, whose registered office is 215 Euston Road,
> London, NW1 2BE.
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> [lists.sourceforge.net]
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_gmod-2Dajax&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=X9VPYUGy4ibZarh9Rup1XaZ62i2u-I0xOZXEy11dXDM&m=2h4i5rjVAcMUOLuJG5ET8RL8r1px37m0nkj5yAy1VdKoa8DBqDWo4DqgwkuPfpJp&s=_T5ACLam-8aQRKMlkktsC7WaVci2zsSyX_BZVxiwRbo&e=>
>
> -- The Wellcome Sanger Institute is operated by Genome Research Limited, a
> charity registered in England with number 1021457 and a company registered
> in England with number 2742969, whose registered office is 215 Euston Road,
> London, NW1 2BE.
>

Re: [Gmod-ajax] hic track on jb2 [EXT]

[Ying S. <yy...@sa...>]

Hi Colin,

Thanks for getting back to me.

I am sorry the content has repeatedly shown in differently places, I wasn’t sure where to get immediate help. As addressed in the previous email, JB2 would highly likely used as gEVAL replace, it would become an essential tools in Darwin tree of life, I am eagerly making it fully functionable.

It would be great that bionano plugin is available soon, it would make huge convenience to our genome evaluation work. Please let me know anything we could do at our ends.

I have another question regarding bed file track. Similar issue as it doesn’t show on the browser. The bed file is in gz together with tbi, the content is as below:
scaffold_1           233421 233621
scaffold_1           275958 276158
scaffold_1           891914 892114
scaffold_1           3507111               3507311
scaffold_1           5410752               5410952

I wonder if the name of scaffold has to be capitals?


Kindest
Yumi

From: Colin <col...@gm...>
Date: Thursday, 19 May 2022 at 19:31
To: Ying Sims <yy...@sa...>
Cc: "gmo...@li..." <gmo...@li...>
Subject: Re: [Gmod-ajax] hic track on jb2 [EXT]

Hi Ying,
I think some of this dialog is continued in various other places (github/gitter) but to answer


1) JBrowse 1 plugins will not work with JBrowse 2 unfortunately, but as you have done, a request for support is here https://github.com/GMOD/jbrowse-components/issues/2962 [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_GMOD_jbrowse-2Dcomponents_issues_2962&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=X9VPYUGy4ibZarh9Rup1XaZ62i2u-I0xOZXEy11dXDM&m=2h4i5rjVAcMUOLuJG5ET8RL8r1px37m0nkj5yAy1VdKoa8DBqDWo4DqgwkuPfpJp&s=VE2KzZVtvhWMDUrKzKZ4pJZpopf4Gt2dThdSQ5fbUgw&e=> :)
2) I think you said that this was resolved, now, by making the scaffold names match the FASTA, but let us know if you have any other concerns


-Colin

On Thu, May 19, 2022 at 9:44 AM Ying Sims <yy...@sa...<mailto:yy...@sa...>> wrote:
Hello,

I am a bioinformatician works on the Darwin Tree of life project in Sanger institute (https://www.darwintreeoflife.org/). I am currently investigating jbrowse2 functionality, and think it could potentially replace our dated genome curation platform(gEVAL).  I have a couple of questions/problem would like to have your help.


  1.  I noticed bionano plugin is available, I also noticed the plugin was developed in 2016, would it work in jb2?
  2.  I use jbrowse cli to load the tracks and assembly. Assembly fasta loads fine,  but bed files and hic files are problematic for me. The hic track doesn't show at all. I have changed the scaffold name in the fasta to capitals but still nothing showed. The following is the command I used to load the hic file. The hic can be displayed in juicebox as I have checked.

jbrowse add-track ~/data/bPtePen1_1/bPtePen1_1_arima.hic -l symlink -a bPtePen1_1



and in the json:

"tracks": [

    {

      "type": "HicTrack",

      "trackId": "bPtePen1_1_arima",

      "name": "bPtePen1_1_arima",

      "adapter": {

        "type": "HicAdapter",

        "hicLocation": {

          "uri": "bPtePen1_1_arima.hic",

          "locationType": "UriLocation"

        }

      },

      "assemblyNames": [

        "bPtePen1_1"

      ]



Could you please help





Kind regards

Yumi
-- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
_______________________________________________
Gmod-ajax mailing list
Gmo...@li...<mailto:Gmo...@li...>
https://lists.sourceforge.net/lists/listinfo/gmod-ajax [lists.sourceforge.net]<https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_gmod-2Dajax&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=X9VPYUGy4ibZarh9Rup1XaZ62i2u-I0xOZXEy11dXDM&m=2h4i5rjVAcMUOLuJG5ET8RL8r1px37m0nkj5yAy1VdKoa8DBqDWo4DqgwkuPfpJp&s=_T5ACLam-8aQRKMlkktsC7WaVci2zsSyX_BZVxiwRbo&e=>



-- 
 The Wellcome Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.

Re: [Gmod-ajax] hic track on jb2

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

Hi Ying,
I think some of this dialog is continued in various other places
(github/gitter) but to answer


1) JBrowse 1 plugins will not work with JBrowse 2 unfortunately, but as you
have done, a request for support is here
https://github.com/GMOD/jbrowse-components/issues/2962 :)
2) I think you said that this was resolved, now, by making the scaffold
names match the FASTA, but let us know if you have any other concerns


-Colin

On Thu, May 19, 2022 at 9:44 AM Ying Sims <yy...@sa...> wrote:

> Hello,
>
>
>
> I am a bioinformatician works on the Darwin Tree of life project in Sanger
> institute (https://www.darwintreeoflife.org/). I am currently
> investigating jbrowse2 functionality, and think it could potentially
> replace our dated genome curation platform(gEVAL).  I have a couple of
> questions/problem would like to have your help.
>
>
>
>    1. I noticed bionano plugin is available, I also noticed the plugin
>    was developed in 2016, would it work in jb2?
>    2. I use jbrowse cli to load the tracks and assembly. Assembly fasta
>    loads fine,  but bed files and hic files are problematic for me. The hic
>    track doesn't show at all. I have changed the scaffold name in the fasta to
>    capitals but still nothing showed. The following is the command I used to
>    load the hic file. The hic can be displayed in juicebox as I have checked.
>
> *jbrowse add-track ~/data/bPtePen1_1/bPtePen1_1_arima.hic -l symlink -a
> bPtePen1_1*
>
>
>
> *and in the json: *
>
> *"tracks": [*
>
> *    {*
>
> *      "type": "HicTrack",*
>
> *      "trackId": "bPtePen1_1_arima",*
>
> *      "name": "bPtePen1_1_arima",*
>
> *      "adapter": {*
>
> *        "type": "HicAdapter",*
>
> *        "hicLocation": {*
>
> *          "uri": "bPtePen1_1_arima.hic",*
>
> *          "locationType": "UriLocation"*
>
> *        }*
>
> *      },*
>
> *      "assemblyNames": [*
>
> *        "bPtePen1_1"*
>
> *      ]*
>
>
>
> Could you please help
>
>
>
>
>
> Kind regards
>
> Yumi
> -- The Wellcome Sanger Institute is operated by Genome Research Limited, a
> charity registered in England with number 1021457 and a company registered
> in England with number 2742969, whose registered office is 215 Euston Road,
> London, NW1 2BE.
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] hic track on jb2

[Ying S. <yy...@sa...>]

Hello,

I am a bioinformatician works on the Darwin Tree of life project in Sanger institute (https://www.darwintreeoflife.org/). I am currently investigating jbrowse2 functionality, and think it could potentially replace our dated genome curation platform(gEVAL).  I have a couple of questions/problem would like to have your help.


  1.  I noticed bionano plugin is available, I also noticed the plugin was developed in 2016, would it work in jb2?
  2.  I use jbrowse cli to load the tracks and assembly. Assembly fasta loads fine,  but bed files and hic files are problematic for me. The hic track doesn't show at all. I have changed the scaffold name in the fasta to capitals but still nothing showed. The following is the command I used to load the hic file. The hic can be displayed in juicebox as I have checked.

jbrowse add-track ~/data/bPtePen1_1/bPtePen1_1_arima.hic -l symlink -a bPtePen1_1



and in the json:

"tracks": [

    {

      "type": "HicTrack",

      "trackId": "bPtePen1_1_arima",

      "name": "bPtePen1_1_arima",

      "adapter": {

        "type": "HicAdapter",

        "hicLocation": {

          "uri": "bPtePen1_1_arima.hic",

          "locationType": "UriLocation"

        }

      },

      "assemblyNames": [

        "bPtePen1_1"

      ]



Could you please help





Kind regards

Yumi



-- 
 The Wellcome Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.

Re: [Gmod-ajax] Synteny Viewer

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

Hi Hans, I'm not aware of anything for jbrowse 1 but we would certainly be
happy to help with jbrowse 2. Currently the synteny view in jbrowse 2 can
compare just two genomes at a time, but definitely interested in extending
this

It could be helpful to know that jbrowse 2 can load the anchors file from
the mcscan pipeline
https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version) also which
I think your figure refers to

-Colin

On Thu, May 19, 2022, 12:07 AM Hans Vasquez-Gross <hva...@un...>
wrote:

> Hello All,
>
> I have a couple questions regarding Synteny visualization. I saw that
> JBrowse2 has a dot plot and linear view for synteny. Are there similar
> plugins for JBrowse1? Currently, I am running JBrowse1, but I am willing to
> also install JBrowse2 for this project.
>
> In the linear view, is there a way to have multiple genomes visualized? I
> have a denovo assembly of haplotype phased data (2 FASTA files) as well as
> a closely related denovo assembly, that I would like to visualize with the
> Sorghum reference.
>
> I found another program that can generate a figure with multiple genomes (
> example
> <https://camo.githubusercontent.com/833e373b369f1c221132d729e1cf0128a8cd638fc04c90782ad7d5e9d30867db/68747470733a2f2f7777772e64726f70626f782e636f6d2f732f39766c337973336e6476696d6734632f67726170652d70656163682d636163616f2e706e673f7261773d31>),
> but was wondering if JBrowse2 can do this.
>
> Thank you,
> -Hans
>
> --
>
>
>
> [image: signature_998258195]
>
> *Hans Vasquez-Gross, Ph.D*
>
> Bioinformatics Scientist,
> Nevada Bioinformatics Center
>
> https://www.unr.edu/bioinformatics
>
> hva...@un...
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] Synteny Viewer

[Hans Vasquez-G. <hva...@un...>]

Hello All,

I have a couple questions regarding Synteny visualization. I saw that JBrowse2 has a dot plot and linear view for synteny. Are there similar plugins for JBrowse1? Currently, I am running JBrowse1, but I am willing to also install JBrowse2 for this project.

In the linear view, is there a way to have multiple genomes visualized? I have a denovo assembly of haplotype phased data (2 FASTA files) as well as a closely related denovo assembly, that I would like to visualize with the Sorghum reference.

I found another program that can generate a figure with multiple genomes (example<https://camo.githubusercontent.com/833e373b369f1c221132d729e1cf0128a8cd638fc04c90782ad7d5e9d30867db/68747470733a2f2f7777772e64726f70626f782e636f6d2f732f39766c337973336e6476696d6734632f67726170652d70656163682d636163616f2e706e673f7261773d31>), but was wondering if JBrowse2 can do this.

Thank you,
-Hans


--



[signature_998258195]

Hans Vasquez-Gross, Ph.D

Bioinformatics Scientist,
Nevada Bioinformatics Center

https://www.unr.edu/bioinformatics

hva...@un...<mailto:hva...@un...>

Re: [Gmod-ajax] I cannot use the UCSC plugin

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

> My aim is to have a genome browser as similar to UCSC as possible (hg38),

It might be cool if we had more examples of loading hg38 data from UCSC. In
JBrowse 1 we had the ucsc-to-json script which was cool and could perform a
bulk import of tracks from UCSC. The UCSCPlugin and trackhubs fill a
similar role in JBrowse 2 but we could probably create a more fleshed out
example

> ...like having the gene name instead of ENSG symbol, and hovering each
transcript and getting info about it and not just the whole gene area.

If you are loading from GFF (UCSC doesn't provide GFF files, but, NCBI,
Ensembl, and others do), then JBrowse will use the Name= or ID= field in
the GFF. If there is a different field e.g. gene_name or something it might
require custom config

Example of using gene_name for the feature labels
https://github.com/GMOD/jbrowse-components/blob/main/test_data/config_demo.json#L194-L205


>I also saw that when I upload a file to be presented as a track (web
mostly, not sure now if also on the standalone app installed on my local
computer), and I come back later, it "disappears" and I have some error
that I should upload the track file again to make it work again, is there
an option to have it there all the time?

If you are using JBrowse Desktop, this problem does not exist, but for
JBrowse Web, we don't have a way to do this yet. It is tricky because the
browser does not have standardized APIs for it, but our desktop app does
let you revisit your files



-Colin

On Tue, May 10, 2022 at 12:43 AM Miri Michaeli <
mir...@an...> wrote:

> Hi Colin,
> First of all, thank you very much for the detailed answer. My aim is to
> have a genome browser as similar to UCSC as possible (hg38), like having
> the gene name instead of ENSG symbol, and hovering each transcript and
> getting info about it and not just the whole gene area.
> But the main goal is to be able to load specific tracks that I prepare (or
> download, such as polyadenylation sites, motifs etc) - either together on
> the same view, or to change the tracks presented to the user, by some
> demand. I am new to working with the config, so taking baby steps here.
> I also saw that when I upload a file to be presented as a track (web
> mostly, not sure now if also on the standalone app installed on my local
> computer), and I come back later, it "disappears" and I have some error
> that I should upload the track file again to make it work again, is there
> an option to have it there all the time?
> I hope I was clear about my goals here.. I like your tool and I hope to be
> able to get to know how to work it around such that I make the best out of
> it!
> Thanks again,
> Miri
>
> On Wed, May 4, 2022 at 1:58 AM Colin <col...@gm...> wrote:
>
>> IRONSCALES couldn't recognize this email as this is the first time you
>> received an email from this sender colin.diesh @ gmail.com
>>
>> And to be clear, the UCSC REST API is different from the UCSC track hubs
>> and the UCSCPlugin can only really  be used when you are manually editing
>> the config file at the moment (doesn't have any extra GUI to pick and
>> choose tracks, so the SegDups example above was made by editing the
>> config.json file, like this
>> https://github.com/GMOD/jbrowse-components/blob/main/test_data/config_demo.json#L268-L278
>> )
>>
>> -Colin
>>
>> On Tue, May 3, 2022 at 4:55 PM Colin <col...@gm...> wrote:
>>
>>> Hi there
>>> Can you describe what your end goal is? Is it to access tracks from UCSC
>>> on hg19 or hg38 (these aren't generally available as a trackhub), or to
>>> access a specific trackhub?
>>>
>>> I just ask because you mention wanting to create a hub.txt but without
>>> knowing what you want it is hard to advise
>>>
>>> Note:
>>>
>>> The trackhubs we connect to are generally from resources that have a
>>> hub.txt e.g. from this list https://genome.ucsc.edu/cgi-bin/hgHubConnect
>>>
>>>
>>> Also, it is a bit confusing but the UCSCPlugin is used for accessing the
>>> UCSC REST API http://genome.ucsc.edu/goldenPath/help/api.html and this
>>> can actually access hg19 and hg38 tracks (example link showing the SegDups
>>> track from UCSC)
>>> https://jbrowse.org/code/jb2/v1.7.6/?config=test_data%2Fconfig_demo.json&session=share-P44nyEajyD&password=iO0Q7
>>>
>>> -Colin
>>>
>>> On Mon, May 2, 2022 at 1:39 PM Miri Michaeli <
>>> mir...@an...> wrote:
>>>
>>>> Hello Jbrowse team!
>>>> I tried several manuals and used almost all the info I could reach out
>>>> to, but I got a dead-end, so I send you this desperate email in request for
>>>> help.
>>>> I installed the UCSC plugin
>>>> [image: image.png]
>>>> then to use it I do:
>>>> [image: image.png]
>>>> but I cannot find how to create a hub.txt even on UCSC they only have
>>>> an example that they claim to work but I downloaded and it doesn't.
>>>> I would appreciate any help because I have struggled with it for a long
>>>> time..
>>>> Thanks in advance,
>>>> Miri
>>>>
>>>> --
>>>> *Miri Michaeli*, PhD
>>>> Bioinformatician Scientist
>>>>
>>>>
>>>>
>>>>
>>>> 10 Hanechoshet St., 2nd Floor
>>>> Tel Aviv, 6971072
>>>> Israel
>>>> mir...@an... <sh...@an...>
>>>> Phone Number: +972-52-4583610
>>>> www.animabiotech.com
>>>>
>>>>
>>>> --------------------------------------
>>>> The content of this email is confidential and intended for the
>>>> recipient specified in message only. It is strictly forbidden to share any
>>>> part of this message with any third party, without a written consent of the
>>>> sender. If you received this message by mistake, please reply to this
>>>> message and follow with its deletion, so that we can ensure such a mistake
>>>> does not occur in the future.
>>>> _______________________________________________
>>>> Gmod-ajax mailing list
>>>> Gmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>
>>>
>
> --
> *Miri Michaeli*, PhD
> Bioinformatician Scientist
>
>
>
>
> 10 Hanechoshet St., 2nd Floor
> Tel Aviv, 6971072
> Israel
> mir...@an... <sh...@an...>
> Phone Number: +972-52-4583610
> www.animabiotech.com
>
>
> --------------------------------------
> The content of this email is confidential and intended for the recipient
> specified in message only. It is strictly forbidden to share any part of
> this message with any third party, without a written consent of the sender.
> If you received this message by mistake, please reply to this message and
> follow with its deletion, so that we can ensure such a mistake does not
> occur in the future.

[Gmod-ajax] Apollo 2.6.6 released

[Garrett S. <ste...@gm...>]

Apollo 2.6.6 has been released:
https://github.com/GMOD/Apollo/releases/tag/2.6.6

*Features*

   - Update Docker container to use Ubuntu 20.04 as the base image (was
   18.04). Thanks @christabone <https://github.com/christabone>. 2645
   <https://github.com/GMOD/Apollo/pull/2645>

*Bug Fixes*

   - Fix typo in Docker docs. Thanks @christabone
   <https://github.com/christabone>. 2638
   <https://github.com/GMOD/Apollo/pull/2638>
   - Use fmin and fmax instead of 3' and 5' in the UI when marking feature
   ends as partial. This more accurately reflects how Apollo stores the data
   about partials. 2646 <https://github.com/GMOD/Apollo/pull/2646>

Full change long for all versions can be found here:
https://github.com/GMOD/Apollo/blob/develop/ChangeLog.md

Docker builds are on docker hub: https://hub.docker.com/r/gmod/apollo

Please review the documentation pages for more details:
http://genomearchitect.readthedocs.io/en/latest/

Note: You can find a guide to upgrading existing Apollo installations here:
https://genomearchitect.readthedocs.io/en/latest/Migration.html

Report issues if found.
Active mailing list (ap...@lb...) and google group
<https://groups.google.com/a/lbl.gov/g/apollo>.

Re: [Gmod-ajax] JBrowse remote files with CORS config

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

Hey Scott,

Thanks so much, that was it!  I was only using a GFF3 as a test but the end result was to use it for bigWigs and other large files which are usually always accessed by URL even if it's local.  I tested those files and they worked fine.

Thanks,

Vaneet
________________________________
From: Scott Cain <sc...@sc...>
Sent: May 2, 2022 4:44 PM
To: Vaneet Lotay <van...@uc...>
Cc: gmo...@li... <gmo...@li...>
Subject: Re: [Gmod-ajax] JBrowse remote files with CORS config

[△EXTERNAL]


Hi Vaneet,

I suspect the problem is with this:

         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "urlTemplate" : "https://ftp.xenbase.org/pub/Genomics/JGI/Xenla9.2/XENLA_9.2_Xenbase_longest.gff3",

You give a url to a GFF file, but you specified the storeClass as NCList, so the urlTemplate should look something like this:

   https://ftp.xenbase.org/pub/Genomics/JGI/Xenla9.2/<https://ftp.xenbase.org/pub/Genomics/JGI/Xenla9.2/XENLA_9.2_Xenbase_longest.gff3>{refseq}/trackData.json

So, the message about json and M is because you can't have an "M" in the first character of a json file.  You either need to bgzip/tabix index this GFF file and change the urlTemplate to put at that bgzip file, or use flatfile_to_json.pl<http://flatfile_to_json.pl> to convert the GFF file to NCList, which will give you a set of directories with the trackData.json at the top of it and modify the urlTemplate to point at it.

Scott


On Mon, May 2, 2022 at 3:08 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hey Scott,

Sorry sending the trackList would be more helpful of course.
Here's the stanza for the track I'm trying to load remotely:

      {
         "style" : {
            "className" : "feature"
         },
         "menuTemplate" : [
            {},
            {},
            {
               "iconClass" : "dijitIconBookmark",
               "content" : "function(track,feature){return track.browser.plugins.FeatureSequence.callFxn(track, feature); }",
               "action" : "contentDialog",
               "label" : "View Feature Sequence"
            }
         ],
         "key" : "Xenopus laevis 9.2-Xenbase (longest)",
         "impliedUTRs" : true,
         "trackType" : "CanvasFeatures",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "urlTemplate" : "https://ftp.xenbase.org/pub/Genomics/JGI/Xenla9.2/XENLA_9.2_Xenbase_longest.gff3",
         "compress" : 0,
         "type" : "CanvasFeatures",
         "category" : "Gene models",
         "label" : "XL9_2_Xenbase_long"
      },

I can certainly send you a simplified complete JSON file after if that's better however I think I found a more helpful clue.  It doesn't seem to be a problem with my trackList JSON file, it's more with the file it's fetching.  The reason I think so is the syntax error it complains about is always the first character of the remote GFF3 file.  This syntax error complains about token 'M' since the file starts with the sequence ID 'MT' for mitochondrial.  If I tried another GFF3, it complains about token '#' since many GFF3 files like the second one I was trying start with commented lines in the header of the file to describe the GFF type and when the file was produced.

Do you know why it would have trouble parsing the file like this?  Otherwise if I'm on the wrong track I'll find a way to send you the complete trackList file, but it seems like it's not the source JSON that's the issue since if I change that one line back to a local URL, there are no errors.

Thanks,

Vaneet
________________________________
From: Scott Cain <sc...@sc...<mailto:sc...@sc...>>
Sent: May 2, 2022 3:28 PM
To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>
Cc: gmo...@li...<mailto:gmo...@li...> <gmo...@li...<mailto:gmo...@li...>>
Subject: Re: [Gmod-ajax] JBrowse remote files with CORS config

[△EXTERNAL]


Hi Vaneet,

It's a little hard to debug a syntax error without seeing the syntax :-)

If you could share your trackList.json or even better, a simplified trackList.json that reproduces the error that would be great. It seems like the most likely cause is a typo.

Scott


On Mon, May 2, 2022 at 1:26 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hey Scott,

Thanks for the help.  Seems like I forgot to restart the apache server to make sure the changes had been compiled. I also made sure the headers module was loaded in apache.

So now it seems that it doesn't work when I try and load the remote track in my trackList.json file but when I try to add it as a custom track via the 'open track file or URL' menu option in JBrowse and choose remote file then it works fine after loading.  Do you know why that would occur?  Here's the error I get when I try loading the remote GFF3 file in my trackList.json:

at XMLHttpRequest.onLoad (webpack:///./node_modules/dojo/request/xhr.js?:126:9) SyntaxError: Unexpected token M in JSON at position 0

All I did was replace the urlTemplate field in my JSON file with the https address for my remote server, was there any additional configuration steps needed?

Thanks,

Vaneet
________________________________
From: Scott Cain <sc...@sc...<mailto:sc...@sc...>>
Sent: April 28, 2022 5:53 PM
To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>
Cc: gmo...@li...<mailto:gmo...@li...> <gmo...@li...<mailto:gmo...@li...>>
Subject: Re: [Gmod-ajax] JBrowse remote files with CORS config

[△EXTERNAL]


Hi Vaneet,

A few years ago I played with CORS and apache, and I used this, which I suspect worked, but I honestly don't remember:

#CORS support (check with Todd if this is OK)
<IfModule mod_headers.c>
   SetEnvIf Origin ^(https?://.+\.wormbase.org<http://wormbase.org>(?::\d{1,5})?)$   CORS_ALLOW_ORIGIN=$1
   Header append Access-Control-Allow-Origin  %{CORS_ALLOW_ORIGIN}e   env=CORS_ALLOW_ORIGIN
   Header onsuccess set Access-Control-Allow-Headers X-Requested-With,Range
   Header merge  Vary "Origin"
</IfModule>

I feel like there is extra junk in here, but certainly the Header lines are probably needed.

Scott


On Thu, Apr 28, 2022 at 3:00 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hey Scott,

Sorry I should have specified, I'm trying to test this in an Apache virtual machine first and then if it works I will try in an AWS bucket perhaps as we're toying with the idea of migrating some of our servers on the cloud.  However, this info is very useful when I get to that step, thank you!

Do you know how this setup would work for Apache?  I was attempting to add the necessary configuration files to the httpd.conf file, does that makes sense?  I'm still getting an error in the browser:

...... has been blocked by CORS policy: No 'Access-Control-Allow-Origin' header is present on the requested resource. If an opaque response serves your needs, set the request's mode to 'no-cors' to fetch the resource with CORS disabled.

I did add an Access-Control-Allow-Origin configuration line with '*' to allow all origins but perhaps I didn't write it correctly.

Thanks,

Vaneet
________________________________
From: Scott Cain <sc...@sc...<mailto:sc...@sc...>>
Sent: April 28, 2022 3:45 PM
To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>
Cc: gmo...@li...<mailto:gmo...@li...> <gmo...@li...<mailto:gmo...@li...>>
Subject: Re: [Gmod-ajax] JBrowse remote files with CORS config

[△EXTERNAL]


Hi Vaneet,

I remember seeing this email a few weeks ago but forgot to answer; thanks for giving me a poke.

There is nothing that needs to be done for anything on the server that is serving up JBrowse, other than making sure you have absolute URLs instead of the more typical relative urls that point at a "local" (to the JBrowse installation) data directory.

For setting up CORS for S3, I know how to do that via the aws command line tool.  Essentially, you can run `aws s3api get-bucket-cors --bucket <name>` which will tell you what the current status of CORS is for the bucket, and then `aws s3api put-bucket-cors --bucket <name> --cors-configuration <json.file>` where the json file will look something like this (which is the one I use for one of our WormBase buckets):

{
    "CORSRules": [
        {
            "AllowedHeaders": [
                "*"
            ],
            "AllowedMethods": [
                "GET"
            ],
            "AllowedOrigins": [
                "*"
            ],
            "ExposeHeaders": [
                "Accept-Ranges",
                "Content-Range",
                "Content-Encoding",
                "Content-Length"
            ],
            "MaxAgeSeconds": 3000
        }
    ]
}

The other item is that the data in the bucket has to be public readable, which means that when you upload the data, you should add `--acl public-read` to the command line `aws s3 cp` command, and I assume there is a similar thing you can do with the web interface, but I don't know how to do that.

Please let me know if this makes sense or if you need any more help,
Scott


On Thu, Apr 14, 2022 at 9:14 AM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hi all,

I'm just wondering if I wanted to load tracks from a remote URL, specifically an HTTPS address, I understand from the documentation that CORS configuration must be setup on the remote server that I'm accessing let's say the bigWig tracks from.  What exactly is involved in that setup, do you simply add the CORS configuration file to the remote server?  If you're working with apache do you simply add it do it's configuration folder?  Are there any other steps involved or is it that simple?  I'm guessing putting a wildcard (*) in the Allowed Origin field allows any server to fetch files from the remote server, but I suppose you can specifiy a specific IP address too?

I did see an example given for configuration related to an Amazon S3 bucket, that would be relevant to me also as I'm contemplating this type of setup as well to store my tracks.

Thanks,

Vaneet
_______________________________________________
Gmod-ajax mailing list
Gmo...@li...<mailto: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/)


--
------------------------------------------------------------------------
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/)


--
------------------------------------------------------------------------
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/)


--
------------------------------------------------------------------------
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] I cannot use the UCSC plugin

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

And to be clear, the UCSC REST API is different from the UCSC track hubs
and the UCSCPlugin can only really  be used when you are manually editing
the config file at the moment (doesn't have any extra GUI to pick and
choose tracks, so the SegDups example above was made by editing the
config.json file, like this
https://github.com/GMOD/jbrowse-components/blob/main/test_data/config_demo.json#L268-L278
)

-Colin

On Tue, May 3, 2022 at 4:55 PM Colin <col...@gm...> wrote:

> Hi there
> Can you describe what your end goal is? Is it to access tracks from UCSC
> on hg19 or hg38 (these aren't generally available as a trackhub), or to
> access a specific trackhub?
>
> I just ask because you mention wanting to create a hub.txt but without
> knowing what you want it is hard to advise
>
> Note:
>
> The trackhubs we connect to are generally from resources that have a
> hub.txt e.g. from this list https://genome.ucsc.edu/cgi-bin/hgHubConnect
>
> Also, it is a bit confusing but the UCSCPlugin is used for accessing the
> UCSC REST API http://genome.ucsc.edu/goldenPath/help/api.html and this
> can actually access hg19 and hg38 tracks (example link showing the SegDups
> track from UCSC)
> https://jbrowse.org/code/jb2/v1.7.6/?config=test_data%2Fconfig_demo.json&session=share-P44nyEajyD&password=iO0Q7
>
> -Colin
>
> On Mon, May 2, 2022 at 1:39 PM Miri Michaeli <
> mir...@an...> wrote:
>
>> Hello Jbrowse team!
>> I tried several manuals and used almost all the info I could reach out
>> to, but I got a dead-end, so I send you this desperate email in request for
>> help.
>> I installed the UCSC plugin
>> [image: image.png]
>> then to use it I do:
>> [image: image.png]
>> but I cannot find how to create a hub.txt even on UCSC they only have an
>> example that they claim to work but I downloaded and it doesn't.
>> I would appreciate any help because I have struggled with it for a long
>> time..
>> Thanks in advance,
>> Miri
>>
>> --
>> *Miri Michaeli*, PhD
>> Bioinformatician Scientist
>>
>>
>>
>>
>> 10 Hanechoshet St., 2nd Floor
>> Tel Aviv, 6971072
>> Israel
>> mir...@an... <sh...@an...>
>> Phone Number: +972-52-4583610
>> www.animabiotech.com
>>
>>
>> --------------------------------------
>> The content of this email is confidential and intended for the recipient
>> specified in message only. It is strictly forbidden to share any part of
>> this message with any third party, without a written consent of the sender.
>> If you received this message by mistake, please reply to this message and
>> follow with its deletion, so that we can ensure such a mistake does not
>> occur in the future._______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

Re: [Gmod-ajax] I cannot use the UCSC plugin

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

Hi there
Can you describe what your end goal is? Is it to access tracks from UCSC on
hg19 or hg38 (these aren't generally available as a trackhub), or to access
a specific trackhub?

I just ask because you mention wanting to create a hub.txt but without
knowing what you want it is hard to advise

Note:

The trackhubs we connect to are generally from resources that have a
hub.txt e.g. from this list https://genome.ucsc.edu/cgi-bin/hgHubConnect

Also, it is a bit confusing but the UCSCPlugin is used for accessing the
UCSC REST API http://genome.ucsc.edu/goldenPath/help/api.html and this can
actually access hg19 and hg38 tracks (example link showing the SegDups
track from UCSC)
https://jbrowse.org/code/jb2/v1.7.6/?config=test_data%2Fconfig_demo.json&session=share-P44nyEajyD&password=iO0Q7

-Colin

On Mon, May 2, 2022 at 1:39 PM Miri Michaeli <mir...@an...>
wrote:

> Hello Jbrowse team!
> I tried several manuals and used almost all the info I could reach out to,
> but I got a dead-end, so I send you this desperate email in request for
> help.
> I installed the UCSC plugin
> [image: image.png]
> then to use it I do:
> [image: image.png]
> but I cannot find how to create a hub.txt even on UCSC they only have an
> example that they claim to work but I downloaded and it doesn't.
> I would appreciate any help because I have struggled with it for a long
> time..
> Thanks in advance,
> Miri
>
> --
> *Miri Michaeli*, PhD
> Bioinformatician Scientist
>
>
>
>
> 10 Hanechoshet St., 2nd Floor
> Tel Aviv, 6971072
> Israel
> mir...@an... <sh...@an...>
> Phone Number: +972-52-4583610
> www.animabiotech.com
>
>
> --------------------------------------
> The content of this email is confidential and intended for the recipient
> specified in message only. It is strictly forbidden to share any part of
> this message with any third party, without a written consent of the sender.
> If you received this message by mistake, please reply to this message and
> follow with its deletion, so that we can ensure such a mistake does not
> occur in the future._______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] JBrowse remote files with CORS config

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

Hi Vaneet,

I suspect the problem is with this:

         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "urlTemplate" : "
https://ftp.xenbase.org/pub/Genomics/JGI/Xenla9.2/XENLA_9.2_Xenbase_longest.gff3
",

You give a url to a GFF file, but you specified the storeClass as NCList,
so the urlTemplate should look something like this:

   https://ftp.xenbase.org/pub/Genomics/JGI/Xenla9.2/
<https://ftp.xenbase.org/pub/Genomics/JGI/Xenla9.2/XENLA_9.2_Xenbase_longest.gff3>
{refseq}/trackData.json

So, the message about json and M is because you can't have an "M" in the
first character of a json file.  You either need to bgzip/tabix index this
GFF file and change the urlTemplate to put at that bgzip file, or use
flatfile_to_json.pl to convert the GFF file to NCList, which will give you
a set of directories with the trackData.json at the top of it and modify
the urlTemplate to point at it.

Scott


On Mon, May 2, 2022 at 3:08 PM Vaneet Lotay <van...@uc...>
wrote:

> Hey Scott,
>
> Sorry sending the trackList would be more helpful of course.
> Here's the stanza for the track I'm trying to load remotely:
>
>       {
>          "style" : {
>             "className" : "feature"
>          },
>          "menuTemplate" : [
>             {},
>             {},
>             {
>                "iconClass" : "dijitIconBookmark",
>                "content" : "function(track,feature){return
> track.browser.plugins.FeatureSequence.callFxn(track, feature); }",
>                "action" : "contentDialog",
>                "label" : "View Feature Sequence"
>             }
>          ],
>          "key" : "Xenopus laevis 9.2-Xenbase (longest)",
>          "impliedUTRs" : true,
>          "trackType" : "CanvasFeatures",
>          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
>          "urlTemplate" : "
> https://ftp.xenbase.org/pub/Genomics/JGI/Xenla9.2/XENLA_9.2_Xenbase_longest.gff3
> ",
>          "compress" : 0,
>          "type" : "CanvasFeatures",
>          "category" : "Gene models",
>          "label" : "XL9_2_Xenbase_long"
>       },
>
> I can certainly send you a simplified complete JSON file after if that's
> better however I think I found a more helpful clue.  It doesn't seem to be
> a problem with my trackList JSON file, it's more with the file it's
> fetching.  The reason I think so is the syntax error it complains about is
> always the first character of the remote GFF3 file.  This syntax error
> complains about token 'M' since the file starts with the sequence ID 'MT'
> for mitochondrial.  If I tried another GFF3, it complains about token '#'
> since many GFF3 files like the second one I was trying start with commented
> lines in the header of the file to describe the GFF type and when the file
> was produced.
>
> Do you know why it would have trouble parsing the file like this?
> Otherwise if I'm on the wrong track I'll find a way to send you the
> complete trackList file, but it seems like it's not the source JSON that's
> the issue since if I change that one line back to a local URL, there are no
> errors.
>
> Thanks,
>
> Vaneet
> ------------------------------
> *From:* Scott Cain <sc...@sc...>
> *Sent:* May 2, 2022 3:28 PM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmo...@li... <gmo...@li...>
> *Subject:* Re: [Gmod-ajax] JBrowse remote files with CORS config
>
> [△EXTERNAL]
>
> Hi Vaneet,
>
> It's a little hard to debug a syntax error without seeing the syntax :-)
>
> If you could share your trackList.json or even better, a simplified
> trackList.json that reproduces the error that would be great. It seems like
> the most likely cause is a typo.
>
> Scott
>
>
> On Mon, May 2, 2022 at 1:26 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hey Scott,
>
> Thanks for the help.  Seems like I forgot to restart the apache server to
> make sure the changes had been compiled. I also made sure the headers
> module was loaded in apache.
>
> So now it seems that it doesn't work when I try and load the remote track
> in my trackList.json file but when I try to add it as a custom track via
> the 'open track file or URL' menu option in JBrowse and choose remote file
> then it works fine after loading.  Do you know why that would occur?
> Here's the error I get when I try loading the remote GFF3 file in my
> trackList.json:
>
> at XMLHttpRequest.onLoad
> (webpack:///./node_modules/dojo/request/xhr.js?:126:9) SyntaxError:
> Unexpected token M in JSON at position 0
>
> All I did was replace the urlTemplate field in my JSON file with the https
> address for my remote server, was there any additional configuration steps
> needed?
>
> Thanks,
>
> Vaneet
> ------------------------------
> *From:* Scott Cain <sc...@sc...>
> *Sent:* April 28, 2022 5:53 PM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmo...@li... <gmo...@li...>
> *Subject:* Re: [Gmod-ajax] JBrowse remote files with CORS config
>
> [△EXTERNAL]
>
> Hi Vaneet,
>
> A few years ago I played with CORS and apache, and I used this, which I
> suspect worked, but I honestly don't remember:
>
> #CORS support (check with Todd if this is OK)
> <IfModule mod_headers.c>
>    SetEnvIf Origin ^(https?://.+\.wormbase.org(?::\d{1,5})?)$
> CORS_ALLOW_ORIGIN=$1
>    Header append Access-Control-Allow-Origin  %{CORS_ALLOW_ORIGIN}e
> env=CORS_ALLOW_ORIGIN
>    Header onsuccess set Access-Control-Allow-Headers X-Requested-With,Range
>    Header merge  Vary "Origin"
> </IfModule>
>
> I feel like there is extra junk in here, but certainly the Header lines
> are probably needed.
>
> Scott
>
>
> On Thu, Apr 28, 2022 at 3:00 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hey Scott,
>
> Sorry I should have specified, I'm trying to test this in an Apache
> virtual machine first and then if it works I will try in an AWS bucket
> perhaps as we're toying with the idea of migrating some of our servers on
> the cloud.  However, this info is very useful when I get to that step,
> thank you!
>
> Do you know how this setup would work for Apache?  I was attempting to add
> the necessary configuration files to the httpd.conf file, does that makes
> sense?  I'm still getting an error in the browser:
>
> ...... has been blocked by CORS policy: No 'Access-Control-Allow-Origin'
> header is present on the requested resource. If an opaque response serves
> your needs, set the request's mode to 'no-cors' to fetch the resource with
> CORS disabled.
>
> I did add an Access-Control-Allow-Origin configuration line with '*' to
> allow all origins but perhaps I didn't write it correctly.
>
> Thanks,
>
> Vaneet
> ------------------------------
> *From:* Scott Cain <sc...@sc...>
> *Sent:* April 28, 2022 3:45 PM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmo...@li... <gmo...@li...>
> *Subject:* Re: [Gmod-ajax] JBrowse remote files with CORS config
>
> [△EXTERNAL]
>
> Hi Vaneet,
>
> I remember seeing this email a few weeks ago but forgot to answer; thanks
> for giving me a poke.
>
> There is nothing that needs to be done for anything on the server that is
> serving up JBrowse, other than making sure you have absolute URLs instead
> of the more typical relative urls that point at a "local" (to the JBrowse
> installation) data directory.
>
> For setting up CORS for S3, I know how to do that via the aws command line
> tool.  Essentially, you can run `aws s3api get-bucket-cors --bucket <name>`
> which will tell you what the current status of CORS is for the bucket, and
> then `aws s3api put-bucket-cors --bucket <name> --cors-configuration
> <json.file>` where the json file will look something like this (which is
> the one I use for one of our WormBase buckets):
>
> {
>     "CORSRules": [
>         {
>             "AllowedHeaders": [
>                 "*"
>             ],
>             "AllowedMethods": [
>                 "GET"
>             ],
>             "AllowedOrigins": [
>                 "*"
>             ],
>             "ExposeHeaders": [
>                 "Accept-Ranges",
>                 "Content-Range",
>                 "Content-Encoding",
>                 "Content-Length"
>             ],
>             "MaxAgeSeconds": 3000
>         }
>     ]
> }
>
> The other item is that the data in the bucket has to be public readable,
> which means that when you upload the data, you should add `--acl
> public-read` to the command line `aws s3 cp` command, and I assume there is
> a similar thing you can do with the web interface, but I don't know how to
> do that.
>
> Please let me know if this makes sense or if you need any more help,
> Scott
>
>
> On Thu, Apr 14, 2022 at 9:14 AM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hi all,
>
> I'm just wondering if I wanted to load tracks from a remote URL,
> specifically an HTTPS address, I understand from the documentation that
> CORS configuration must be setup on the remote server that I'm accessing
> let's say the bigWig tracks from.  What exactly is involved in that setup,
> do you simply add the CORS configuration file to the remote server?  If
> you're working with apache do you simply add it do it's configuration
> folder?  Are there any other steps involved or is it that simple?  I'm
> guessing putting a wildcard (*) in the Allowed Origin field allows any
> server to fetch files from the remote server, but I suppose you can
> specifiy a specific IP address too?
>
> I did see an example given for configuration related to an Amazon S3
> bucket, that would be relevant to me also as I'm contemplating this type of
> setup as well to store my tracks.
>
> Thanks,
>
> Vaneet
> _______________________________________________
> 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/)
>
>
>
> --
> ------------------------------------------------------------------------
> 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/)
>
>
>
> --
> ------------------------------------------------------------------------
> 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/)
>


-- 
------------------------------------------------------------------------
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] JBrowse remote files with CORS config

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

Hey Scott,

Sorry sending the trackList would be more helpful of course.
Here's the stanza for the track I'm trying to load remotely:

      {
         "style" : {
            "className" : "feature"
         },
         "menuTemplate" : [
            {},
            {},
            {
               "iconClass" : "dijitIconBookmark",
               "content" : "function(track,feature){return track.browser.plugins.FeatureSequence.callFxn(track, feature); }",
               "action" : "contentDialog",
               "label" : "View Feature Sequence"
            }
         ],
         "key" : "Xenopus laevis 9.2-Xenbase (longest)",
         "impliedUTRs" : true,
         "trackType" : "CanvasFeatures",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "urlTemplate" : "https://ftp.xenbase.org/pub/Genomics/JGI/Xenla9.2/XENLA_9.2_Xenbase_longest.gff3",
         "compress" : 0,
         "type" : "CanvasFeatures",
         "category" : "Gene models",
         "label" : "XL9_2_Xenbase_long"
      },

I can certainly send you a simplified complete JSON file after if that's better however I think I found a more helpful clue.  It doesn't seem to be a problem with my trackList JSON file, it's more with the file it's fetching.  The reason I think so is the syntax error it complains about is always the first character of the remote GFF3 file.  This syntax error complains about token 'M' since the file starts with the sequence ID 'MT' for mitochondrial.  If I tried another GFF3, it complains about token '#' since many GFF3 files like the second one I was trying start with commented lines in the header of the file to describe the GFF type and when the file was produced.

Do you know why it would have trouble parsing the file like this?  Otherwise if I'm on the wrong track I'll find a way to send you the complete trackList file, but it seems like it's not the source JSON that's the issue since if I change that one line back to a local URL, there are no errors.

Thanks,

Vaneet
________________________________
From: Scott Cain <sc...@sc...>
Sent: May 2, 2022 3:28 PM
To: Vaneet Lotay <van...@uc...>
Cc: gmo...@li... <gmo...@li...>
Subject: Re: [Gmod-ajax] JBrowse remote files with CORS config

[△EXTERNAL]


Hi Vaneet,

It's a little hard to debug a syntax error without seeing the syntax :-)

If you could share your trackList.json or even better, a simplified trackList.json that reproduces the error that would be great. It seems like the most likely cause is a typo.

Scott


On Mon, May 2, 2022 at 1:26 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hey Scott,

Thanks for the help.  Seems like I forgot to restart the apache server to make sure the changes had been compiled. I also made sure the headers module was loaded in apache.

So now it seems that it doesn't work when I try and load the remote track in my trackList.json file but when I try to add it as a custom track via the 'open track file or URL' menu option in JBrowse and choose remote file then it works fine after loading.  Do you know why that would occur?  Here's the error I get when I try loading the remote GFF3 file in my trackList.json:

at XMLHttpRequest.onLoad (webpack:///./node_modules/dojo/request/xhr.js?:126:9) SyntaxError: Unexpected token M in JSON at position 0

All I did was replace the urlTemplate field in my JSON file with the https address for my remote server, was there any additional configuration steps needed?

Thanks,

Vaneet
________________________________
From: Scott Cain <sc...@sc...<mailto:sc...@sc...>>
Sent: April 28, 2022 5:53 PM
To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>
Cc: gmo...@li...<mailto:gmo...@li...> <gmo...@li...<mailto:gmo...@li...>>
Subject: Re: [Gmod-ajax] JBrowse remote files with CORS config

[△EXTERNAL]


Hi Vaneet,

A few years ago I played with CORS and apache, and I used this, which I suspect worked, but I honestly don't remember:

#CORS support (check with Todd if this is OK)
<IfModule mod_headers.c>
   SetEnvIf Origin ^(https?://.+\.wormbase.org<http://wormbase.org>(?::\d{1,5})?)$   CORS_ALLOW_ORIGIN=$1
   Header append Access-Control-Allow-Origin  %{CORS_ALLOW_ORIGIN}e   env=CORS_ALLOW_ORIGIN
   Header onsuccess set Access-Control-Allow-Headers X-Requested-With,Range
   Header merge  Vary "Origin"
</IfModule>

I feel like there is extra junk in here, but certainly the Header lines are probably needed.

Scott


On Thu, Apr 28, 2022 at 3:00 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hey Scott,

Sorry I should have specified, I'm trying to test this in an Apache virtual machine first and then if it works I will try in an AWS bucket perhaps as we're toying with the idea of migrating some of our servers on the cloud.  However, this info is very useful when I get to that step, thank you!

Do you know how this setup would work for Apache?  I was attempting to add the necessary configuration files to the httpd.conf file, does that makes sense?  I'm still getting an error in the browser:

...... has been blocked by CORS policy: No 'Access-Control-Allow-Origin' header is present on the requested resource. If an opaque response serves your needs, set the request's mode to 'no-cors' to fetch the resource with CORS disabled.

I did add an Access-Control-Allow-Origin configuration line with '*' to allow all origins but perhaps I didn't write it correctly.

Thanks,

Vaneet
________________________________
From: Scott Cain <sc...@sc...<mailto:sc...@sc...>>
Sent: April 28, 2022 3:45 PM
To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>
Cc: gmo...@li...<mailto:gmo...@li...> <gmo...@li...<mailto:gmo...@li...>>
Subject: Re: [Gmod-ajax] JBrowse remote files with CORS config

[△EXTERNAL]


Hi Vaneet,

I remember seeing this email a few weeks ago but forgot to answer; thanks for giving me a poke.

There is nothing that needs to be done for anything on the server that is serving up JBrowse, other than making sure you have absolute URLs instead of the more typical relative urls that point at a "local" (to the JBrowse installation) data directory.

For setting up CORS for S3, I know how to do that via the aws command line tool.  Essentially, you can run `aws s3api get-bucket-cors --bucket <name>` which will tell you what the current status of CORS is for the bucket, and then `aws s3api put-bucket-cors --bucket <name> --cors-configuration <json.file>` where the json file will look something like this (which is the one I use for one of our WormBase buckets):

{
    "CORSRules": [
        {
            "AllowedHeaders": [
                "*"
            ],
            "AllowedMethods": [
                "GET"
            ],
            "AllowedOrigins": [
                "*"
            ],
            "ExposeHeaders": [
                "Accept-Ranges",
                "Content-Range",
                "Content-Encoding",
                "Content-Length"
            ],
            "MaxAgeSeconds": 3000
        }
    ]
}

The other item is that the data in the bucket has to be public readable, which means that when you upload the data, you should add `--acl public-read` to the command line `aws s3 cp` command, and I assume there is a similar thing you can do with the web interface, but I don't know how to do that.

Please let me know if this makes sense or if you need any more help,
Scott


On Thu, Apr 14, 2022 at 9:14 AM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hi all,

I'm just wondering if I wanted to load tracks from a remote URL, specifically an HTTPS address, I understand from the documentation that CORS configuration must be setup on the remote server that I'm accessing let's say the bigWig tracks from.  What exactly is involved in that setup, do you simply add the CORS configuration file to the remote server?  If you're working with apache do you simply add it do it's configuration folder?  Are there any other steps involved or is it that simple?  I'm guessing putting a wildcard (*) in the Allowed Origin field allows any server to fetch files from the remote server, but I suppose you can specifiy a specific IP address too?

I did see an example given for configuration related to an Amazon S3 bucket, that would be relevant to me also as I'm contemplating this type of setup as well to store my tracks.

Thanks,

Vaneet
_______________________________________________
Gmod-ajax mailing list
Gmo...@li...<mailto: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/)


--
------------------------------------------------------------------------
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/)


--
------------------------------------------------------------------------
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] About downloading sequence out of gene body

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

Hi there,
If you use the "highlight tool" or go to the menu bar and hit View->Set
highlight, then specify your region

Then, open the sequence track, go to the track menu, and hit "Save data".
This will then let you save the sequence of the highlighted region

Screenshot attached
-Colin

On Mon, May 2, 2022 at 1:39 PM Dai, Dawei <daw...@uf...> wrote:

> Hi,
>
> I would like to ask a question about how to download the sequence out of
> maize gene body in multiple genomes.
>
> For example, I would like to download the region from *multiple maize
> lines indicated with a red box*, but I can not find a way to download
> those.
>
>
>
> Sincerely,
> Dawei
>
> *------------------------------------------------------- *
> *Dawei Dai *
> Plant Cell & Molecular Biology Laboratory
> Horticultural Sciences Department
> University of Florida
> Gainesville, FL 32611
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] JBrowse remote files with CORS config

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

Hi Vaneet,

It's a little hard to debug a syntax error without seeing the syntax :-)

If you could share your trackList.json or even better, a simplified
trackList.json that reproduces the error that would be great. It seems like
the most likely cause is a typo.

Scott


On Mon, May 2, 2022 at 1:26 PM Vaneet Lotay <van...@uc...>
wrote:

> Hey Scott,
>
> Thanks for the help.  Seems like I forgot to restart the apache server to
> make sure the changes had been compiled. I also made sure the headers
> module was loaded in apache.
>
> So now it seems that it doesn't work when I try and load the remote track
> in my trackList.json file but when I try to add it as a custom track via
> the 'open track file or URL' menu option in JBrowse and choose remote file
> then it works fine after loading.  Do you know why that would occur?
> Here's the error I get when I try loading the remote GFF3 file in my
> trackList.json:
>
> at XMLHttpRequest.onLoad
> (webpack:///./node_modules/dojo/request/xhr.js?:126:9) SyntaxError:
> Unexpected token M in JSON at position 0
>
> All I did was replace the urlTemplate field in my JSON file with the https
> address for my remote server, was there any additional configuration steps
> needed?
>
> Thanks,
>
> Vaneet
> ------------------------------
> *From:* Scott Cain <sc...@sc...>
> *Sent:* April 28, 2022 5:53 PM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmo...@li... <gmo...@li...>
> *Subject:* Re: [Gmod-ajax] JBrowse remote files with CORS config
>
> [△EXTERNAL]
>
> Hi Vaneet,
>
> A few years ago I played with CORS and apache, and I used this, which I
> suspect worked, but I honestly don't remember:
>
> #CORS support (check with Todd if this is OK)
> <IfModule mod_headers.c>
>    SetEnvIf Origin ^(https?://.+\.wormbase.org(?::\d{1,5})?)$
> CORS_ALLOW_ORIGIN=$1
>    Header append Access-Control-Allow-Origin  %{CORS_ALLOW_ORIGIN}e
> env=CORS_ALLOW_ORIGIN
>    Header onsuccess set Access-Control-Allow-Headers X-Requested-With,Range
>    Header merge  Vary "Origin"
> </IfModule>
>
> I feel like there is extra junk in here, but certainly the Header lines
> are probably needed.
>
> Scott
>
>
> On Thu, Apr 28, 2022 at 3:00 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hey Scott,
>
> Sorry I should have specified, I'm trying to test this in an Apache
> virtual machine first and then if it works I will try in an AWS bucket
> perhaps as we're toying with the idea of migrating some of our servers on
> the cloud.  However, this info is very useful when I get to that step,
> thank you!
>
> Do you know how this setup would work for Apache?  I was attempting to add
> the necessary configuration files to the httpd.conf file, does that makes
> sense?  I'm still getting an error in the browser:
>
> ...... has been blocked by CORS policy: No 'Access-Control-Allow-Origin'
> header is present on the requested resource. If an opaque response serves
> your needs, set the request's mode to 'no-cors' to fetch the resource with
> CORS disabled.
>
> I did add an Access-Control-Allow-Origin configuration line with '*' to
> allow all origins but perhaps I didn't write it correctly.
>
> Thanks,
>
> Vaneet
> ------------------------------
> *From:* Scott Cain <sc...@sc...>
> *Sent:* April 28, 2022 3:45 PM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmo...@li... <gmo...@li...>
> *Subject:* Re: [Gmod-ajax] JBrowse remote files with CORS config
>
> [△EXTERNAL]
>
> Hi Vaneet,
>
> I remember seeing this email a few weeks ago but forgot to answer; thanks
> for giving me a poke.
>
> There is nothing that needs to be done for anything on the server that is
> serving up JBrowse, other than making sure you have absolute URLs instead
> of the more typical relative urls that point at a "local" (to the JBrowse
> installation) data directory.
>
> For setting up CORS for S3, I know how to do that via the aws command line
> tool.  Essentially, you can run `aws s3api get-bucket-cors --bucket <name>`
> which will tell you what the current status of CORS is for the bucket, and
> then `aws s3api put-bucket-cors --bucket <name> --cors-configuration
> <json.file>` where the json file will look something like this (which is
> the one I use for one of our WormBase buckets):
>
> {
>     "CORSRules": [
>         {
>             "AllowedHeaders": [
>                 "*"
>             ],
>             "AllowedMethods": [
>                 "GET"
>             ],
>             "AllowedOrigins": [
>                 "*"
>             ],
>             "ExposeHeaders": [
>                 "Accept-Ranges",
>                 "Content-Range",
>                 "Content-Encoding",
>                 "Content-Length"
>             ],
>             "MaxAgeSeconds": 3000
>         }
>     ]
> }
>
> The other item is that the data in the bucket has to be public readable,
> which means that when you upload the data, you should add `--acl
> public-read` to the command line `aws s3 cp` command, and I assume there is
> a similar thing you can do with the web interface, but I don't know how to
> do that.
>
> Please let me know if this makes sense or if you need any more help,
> Scott
>
>
> On Thu, Apr 14, 2022 at 9:14 AM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hi all,
>
> I'm just wondering if I wanted to load tracks from a remote URL,
> specifically an HTTPS address, I understand from the documentation that
> CORS configuration must be setup on the remote server that I'm accessing
> let's say the bigWig tracks from.  What exactly is involved in that setup,
> do you simply add the CORS configuration file to the remote server?  If
> you're working with apache do you simply add it do it's configuration
> folder?  Are there any other steps involved or is it that simple?  I'm
> guessing putting a wildcard (*) in the Allowed Origin field allows any
> server to fetch files from the remote server, but I suppose you can
> specifiy a specific IP address too?
>
> I did see an example given for configuration related to an Amazon S3
> bucket, that would be relevant to me also as I'm contemplating this type of
> setup as well to store my tracks.
>
> Thanks,
>
> Vaneet
> _______________________________________________
> 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/)
>
>
>
> --
> ------------------------------------------------------------------------
> 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/)
>


-- 
------------------------------------------------------------------------
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] JBrowse remote files with CORS config

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

Hey Scott,

Thanks for the help.  Seems like I forgot to restart the apache server to make sure the changes had been compiled. I also made sure the headers module was loaded in apache.

So now it seems that it doesn't work when I try and load the remote track in my trackList.json file but when I try to add it as a custom track via the 'open track file or URL' menu option in JBrowse and choose remote file then it works fine after loading.  Do you know why that would occur?  Here's the error I get when I try loading the remote GFF3 file in my trackList.json:

at XMLHttpRequest.onLoad (webpack:///./node_modules/dojo/request/xhr.js?:126:9) SyntaxError: Unexpected token M in JSON at position 0

All I did was replace the urlTemplate field in my JSON file with the https address for my remote server, was there any additional configuration steps needed?

Thanks,

Vaneet
________________________________
From: Scott Cain <sc...@sc...>
Sent: April 28, 2022 5:53 PM
To: Vaneet Lotay <van...@uc...>
Cc: gmo...@li... <gmo...@li...>
Subject: Re: [Gmod-ajax] JBrowse remote files with CORS config

[△EXTERNAL]


Hi Vaneet,

A few years ago I played with CORS and apache, and I used this, which I suspect worked, but I honestly don't remember:

#CORS support (check with Todd if this is OK)
<IfModule mod_headers.c>
   SetEnvIf Origin ^(https?://.+\.wormbase.org<http://wormbase.org>(?::\d{1,5})?)$   CORS_ALLOW_ORIGIN=$1
   Header append Access-Control-Allow-Origin  %{CORS_ALLOW_ORIGIN}e   env=CORS_ALLOW_ORIGIN
   Header onsuccess set Access-Control-Allow-Headers X-Requested-With,Range
   Header merge  Vary "Origin"
</IfModule>

I feel like there is extra junk in here, but certainly the Header lines are probably needed.

Scott


On Thu, Apr 28, 2022 at 3:00 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hey Scott,

Sorry I should have specified, I'm trying to test this in an Apache virtual machine first and then if it works I will try in an AWS bucket perhaps as we're toying with the idea of migrating some of our servers on the cloud.  However, this info is very useful when I get to that step, thank you!

Do you know how this setup would work for Apache?  I was attempting to add the necessary configuration files to the httpd.conf file, does that makes sense?  I'm still getting an error in the browser:

...... has been blocked by CORS policy: No 'Access-Control-Allow-Origin' header is present on the requested resource. If an opaque response serves your needs, set the request's mode to 'no-cors' to fetch the resource with CORS disabled.

I did add an Access-Control-Allow-Origin configuration line with '*' to allow all origins but perhaps I didn't write it correctly.

Thanks,

Vaneet
________________________________
From: Scott Cain <sc...@sc...<mailto:sc...@sc...>>
Sent: April 28, 2022 3:45 PM
To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>
Cc: gmo...@li...<mailto:gmo...@li...> <gmo...@li...<mailto:gmo...@li...>>
Subject: Re: [Gmod-ajax] JBrowse remote files with CORS config

[△EXTERNAL]


Hi Vaneet,

I remember seeing this email a few weeks ago but forgot to answer; thanks for giving me a poke.

There is nothing that needs to be done for anything on the server that is serving up JBrowse, other than making sure you have absolute URLs instead of the more typical relative urls that point at a "local" (to the JBrowse installation) data directory.

For setting up CORS for S3, I know how to do that via the aws command line tool.  Essentially, you can run `aws s3api get-bucket-cors --bucket <name>` which will tell you what the current status of CORS is for the bucket, and then `aws s3api put-bucket-cors --bucket <name> --cors-configuration <json.file>` where the json file will look something like this (which is the one I use for one of our WormBase buckets):

{
    "CORSRules": [
        {
            "AllowedHeaders": [
                "*"
            ],
            "AllowedMethods": [
                "GET"
            ],
            "AllowedOrigins": [
                "*"
            ],
            "ExposeHeaders": [
                "Accept-Ranges",
                "Content-Range",
                "Content-Encoding",
                "Content-Length"
            ],
            "MaxAgeSeconds": 3000
        }
    ]
}

The other item is that the data in the bucket has to be public readable, which means that when you upload the data, you should add `--acl public-read` to the command line `aws s3 cp` command, and I assume there is a similar thing you can do with the web interface, but I don't know how to do that.

Please let me know if this makes sense or if you need any more help,
Scott


On Thu, Apr 14, 2022 at 9:14 AM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hi all,

I'm just wondering if I wanted to load tracks from a remote URL, specifically an HTTPS address, I understand from the documentation that CORS configuration must be setup on the remote server that I'm accessing let's say the bigWig tracks from.  What exactly is involved in that setup, do you simply add the CORS configuration file to the remote server?  If you're working with apache do you simply add it do it's configuration folder?  Are there any other steps involved or is it that simple?  I'm guessing putting a wildcard (*) in the Allowed Origin field allows any server to fetch files from the remote server, but I suppose you can specifiy a specific IP address too?

I did see an example given for configuration related to an Amazon S3 bucket, that would be relevant to me also as I'm contemplating this type of setup as well to store my tracks.

Thanks,

Vaneet
_______________________________________________
Gmod-ajax mailing list
Gmo...@li...<mailto: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/)


--
------------------------------------------------------------------------
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] About downloading sequence out of gene body

[Dai, D. <daw...@uf...>]

Hi,

I would like to ask a question about how to download the sequence out of maize gene body in multiple genomes.

For example, I would like to download the region from multiple maize lines indicated with a red box, but I can not find a way to download those.

[cid:596952f1-da5c-451f-b791-a689ec7046bf]

Sincerely,
Dawei
-------------------------------------------------------
Dawei Dai
Plant Cell & Molecular Biology Laboratory
Horticultural Sciences Department
University of Florida
Gainesville, FL 32611

[Gmod-ajax] I cannot use the UCSC plugin

[Miri M. <mir...@an...>]

Hello Jbrowse team!
I tried several manuals and used almost all the info I could reach out to,
but I got a dead-end, so I send you this desperate email in request for
help.
I installed the UCSC plugin
[image: image.png]
then to use it I do:
[image: image.png]
but I cannot find how to create a hub.txt even on UCSC they only have an
example that they claim to work but I downloaded and it doesn't.
I would appreciate any help because I have struggled with it for a long
time..
Thanks in advance,
Miri

-- 
*Miri Michaeli*, PhD
Bioinformatician Scientist




10 Hanechoshet St., 2nd Floor
Tel Aviv, 6971072
Israel
mir...@an... <sh...@an...>
Phone Number: +972-52-4583610
www.animabiotech.com

-- 


--------------------------------------
The content of this email is 
confidential and intended for the recipient specified in message only. It 
is strictly forbidden to share any part of this message with any third 
party, without a written consent of the sender. If you received this 
message by mistake, please reply to this message and follow with its 
deletion, so that we can ensure such a mistake does not occur in the future.

Re: [Gmod-ajax] JBrowse remote files with CORS config

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

Hi Vaneet,

A few years ago I played with CORS and apache, and I used this, which I
suspect worked, but I honestly don't remember:

#CORS support (check with Todd if this is OK)
<IfModule mod_headers.c>
   SetEnvIf Origin ^(https?://.+\.wormbase.org(?::\d{1,5})?)$
CORS_ALLOW_ORIGIN=$1
   Header append Access-Control-Allow-Origin  %{CORS_ALLOW_ORIGIN}e
env=CORS_ALLOW_ORIGIN
   Header onsuccess set Access-Control-Allow-Headers X-Requested-With,Range
   Header merge  Vary "Origin"
</IfModule>

I feel like there is extra junk in here, but certainly the Header lines are
probably needed.

Scott


On Thu, Apr 28, 2022 at 3:00 PM Vaneet Lotay <van...@uc...>
wrote:

> Hey Scott,
>
> Sorry I should have specified, I'm trying to test this in an Apache
> virtual machine first and then if it works I will try in an AWS bucket
> perhaps as we're toying with the idea of migrating some of our servers on
> the cloud.  However, this info is very useful when I get to that step,
> thank you!
>
> Do you know how this setup would work for Apache?  I was attempting to add
> the necessary configuration files to the httpd.conf file, does that makes
> sense?  I'm still getting an error in the browser:
>
> ...... has been blocked by CORS policy: No 'Access-Control-Allow-Origin'
> header is present on the requested resource. If an opaque response serves
> your needs, set the request's mode to 'no-cors' to fetch the resource with
> CORS disabled.
>
> I did add an Access-Control-Allow-Origin configuration line with '*' to
> allow all origins but perhaps I didn't write it correctly.
>
> Thanks,
>
> Vaneet
> ------------------------------
> *From:* Scott Cain <sc...@sc...>
> *Sent:* April 28, 2022 3:45 PM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmo...@li... <gmo...@li...>
> *Subject:* Re: [Gmod-ajax] JBrowse remote files with CORS config
>
> [△EXTERNAL]
>
> Hi Vaneet,
>
> I remember seeing this email a few weeks ago but forgot to answer; thanks
> for giving me a poke.
>
> There is nothing that needs to be done for anything on the server that is
> serving up JBrowse, other than making sure you have absolute URLs instead
> of the more typical relative urls that point at a "local" (to the JBrowse
> installation) data directory.
>
> For setting up CORS for S3, I know how to do that via the aws command line
> tool.  Essentially, you can run `aws s3api get-bucket-cors --bucket <name>`
> which will tell you what the current status of CORS is for the bucket, and
> then `aws s3api put-bucket-cors --bucket <name> --cors-configuration
> <json.file>` where the json file will look something like this (which is
> the one I use for one of our WormBase buckets):
>
> {
>     "CORSRules": [
>         {
>             "AllowedHeaders": [
>                 "*"
>             ],
>             "AllowedMethods": [
>                 "GET"
>             ],
>             "AllowedOrigins": [
>                 "*"
>             ],
>             "ExposeHeaders": [
>                 "Accept-Ranges",
>                 "Content-Range",
>                 "Content-Encoding",
>                 "Content-Length"
>             ],
>             "MaxAgeSeconds": 3000
>         }
>     ]
> }
>
> The other item is that the data in the bucket has to be public readable,
> which means that when you upload the data, you should add `--acl
> public-read` to the command line `aws s3 cp` command, and I assume there is
> a similar thing you can do with the web interface, but I don't know how to
> do that.
>
> Please let me know if this makes sense or if you need any more help,
> Scott
>
>
> On Thu, Apr 14, 2022 at 9:14 AM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hi all,
>
> I'm just wondering if I wanted to load tracks from a remote URL,
> specifically an HTTPS address, I understand from the documentation that
> CORS configuration must be setup on the remote server that I'm accessing
> let's say the bigWig tracks from.  What exactly is involved in that setup,
> do you simply add the CORS configuration file to the remote server?  If
> you're working with apache do you simply add it do it's configuration
> folder?  Are there any other steps involved or is it that simple?  I'm
> guessing putting a wildcard (*) in the Allowed Origin field allows any
> server to fetch files from the remote server, but I suppose you can
> specifiy a specific IP address too?
>
> I did see an example given for configuration related to an Amazon S3
> bucket, that would be relevant to me also as I'm contemplating this type of
> setup as well to store my tracks.
>
> Thanks,
>
> Vaneet
> _______________________________________________
> 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/)
>


-- 
------------------------------------------------------------------------
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] JBrowse remote files with CORS config

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

Hey Scott,

Sorry I should have specified, I'm trying to test this in an Apache virtual machine first and then if it works I will try in an AWS bucket perhaps as we're toying with the idea of migrating some of our servers on the cloud.  However, this info is very useful when I get to that step, thank you!

Do you know how this setup would work for Apache?  I was attempting to add the necessary configuration files to the httpd.conf file, does that makes sense?  I'm still getting an error in the browser:

...... has been blocked by CORS policy: No 'Access-Control-Allow-Origin' header is present on the requested resource. If an opaque response serves your needs, set the request's mode to 'no-cors' to fetch the resource with CORS disabled.

I did add an Access-Control-Allow-Origin configuration line with '*' to allow all origins but perhaps I didn't write it correctly.

Thanks,

Vaneet
________________________________
From: Scott Cain <sc...@sc...>
Sent: April 28, 2022 3:45 PM
To: Vaneet Lotay <van...@uc...>
Cc: gmo...@li... <gmo...@li...>
Subject: Re: [Gmod-ajax] JBrowse remote files with CORS config

[△EXTERNAL]


Hi Vaneet,

I remember seeing this email a few weeks ago but forgot to answer; thanks for giving me a poke.

There is nothing that needs to be done for anything on the server that is serving up JBrowse, other than making sure you have absolute URLs instead of the more typical relative urls that point at a "local" (to the JBrowse installation) data directory.

For setting up CORS for S3, I know how to do that via the aws command line tool.  Essentially, you can run `aws s3api get-bucket-cors --bucket <name>` which will tell you what the current status of CORS is for the bucket, and then `aws s3api put-bucket-cors --bucket <name> --cors-configuration <json.file>` where the json file will look something like this (which is the one I use for one of our WormBase buckets):

{
    "CORSRules": [
        {
            "AllowedHeaders": [
                "*"
            ],
            "AllowedMethods": [
                "GET"
            ],
            "AllowedOrigins": [
                "*"
            ],
            "ExposeHeaders": [
                "Accept-Ranges",
                "Content-Range",
                "Content-Encoding",
                "Content-Length"
            ],
            "MaxAgeSeconds": 3000
        }
    ]
}

The other item is that the data in the bucket has to be public readable, which means that when you upload the data, you should add `--acl public-read` to the command line `aws s3 cp` command, and I assume there is a similar thing you can do with the web interface, but I don't know how to do that.

Please let me know if this makes sense or if you need any more help,
Scott


On Thu, Apr 14, 2022 at 9:14 AM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hi all,

I'm just wondering if I wanted to load tracks from a remote URL, specifically an HTTPS address, I understand from the documentation that CORS configuration must be setup on the remote server that I'm accessing let's say the bigWig tracks from.  What exactly is involved in that setup, do you simply add the CORS configuration file to the remote server?  If you're working with apache do you simply add it do it's configuration folder?  Are there any other steps involved or is it that simple?  I'm guessing putting a wildcard (*) in the Allowed Origin field allows any server to fetch files from the remote server, but I suppose you can specifiy a specific IP address too?

I did see an example given for configuration related to an Amazon S3 bucket, that would be relevant to me also as I'm contemplating this type of setup as well to store my tracks.

Thanks,

Vaneet
_______________________________________________
Gmod-ajax mailing list
Gmo...@li...<mailto: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/)

Re: [Gmod-ajax] JBrowse remote files with CORS config

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

Hi Vaneet,

I remember seeing this email a few weeks ago but forgot to answer; thanks
for giving me a poke.

There is nothing that needs to be done for anything on the server that is
serving up JBrowse, other than making sure you have absolute URLs instead
of the more typical relative urls that point at a "local" (to the JBrowse
installation) data directory.

For setting up CORS for S3, I know how to do that via the aws command line
tool.  Essentially, you can run `aws s3api get-bucket-cors --bucket <name>`
which will tell you what the current status of CORS is for the bucket, and
then `aws s3api put-bucket-cors --bucket <name> --cors-configuration
<json.file>` where the json file will look something like this (which is
the one I use for one of our WormBase buckets):

{
    "CORSRules": [
        {
            "AllowedHeaders": [
                "*"
            ],
            "AllowedMethods": [
                "GET"
            ],
            "AllowedOrigins": [
                "*"
            ],
            "ExposeHeaders": [
                "Accept-Ranges",
                "Content-Range",
                "Content-Encoding",
                "Content-Length"
            ],
            "MaxAgeSeconds": 3000
        }
    ]
}

The other item is that the data in the bucket has to be public readable,
which means that when you upload the data, you should add `--acl
public-read` to the command line `aws s3 cp` command, and I assume there is
a similar thing you can do with the web interface, but I don't know how to
do that.

Please let me know if this makes sense or if you need any more help,
Scott


On Thu, Apr 14, 2022 at 9:14 AM Vaneet Lotay <van...@uc...>
wrote:

> Hi all,
>
> I'm just wondering if I wanted to load tracks from a remote URL,
> specifically an HTTPS address, I understand from the documentation that
> CORS configuration must be setup on the remote server that I'm accessing
> let's say the bigWig tracks from.  What exactly is involved in that setup,
> do you simply add the CORS configuration file to the remote server?  If
> you're working with apache do you simply add it do it's configuration
> folder?  Are there any other steps involved or is it that simple?  I'm
> guessing putting a wildcard (*) in the Allowed Origin field allows any
> server to fetch files from the remote server, but I suppose you can
> specifiy a specific IP address too?
>
> I did see an example given for configuration related to an Amazon S3
> bucket, that would be relevant to me also as I'm contemplating this type of
> setup as well to store my tracks.
>
> Thanks,
>
> Vaneet
> _______________________________________________
> 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] JBrowse remote files with CORS config

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

Hi all,

I'm just wondering if I wanted to load tracks from a remote URL, specifically an HTTPS address, I understand from the documentation that CORS configuration must be setup on the remote server that I'm accessing let's say the bigWig tracks from.  What exactly is involved in that setup, do you simply add the CORS configuration file to the remote server?  If you're working with apache do you simply add it do it's configuration folder?  Are there any other steps involved or is it that simple?  I'm guessing putting a wildcard (*) in the Allowed Origin field allows any server to fetch files from the remote server, but I suppose you can specifiy a specific IP address too?

I did see an example given for configuration related to an Amazon S3 bucket, that would be relevant to me also as I'm contemplating this type of setup as well to store my tracks.

Thanks,

Vaneet

Re: [Gmod-ajax] [apollo] search by gene name

[Ulysse G. <ug...@gm...>]

Thanks you, I was Indeed looking to search from within the jbrowse
directory for non-annotated genes. Your solution worked, thanks a lot.
Ulysse


Le ven. 8 avr. 2022 à 19:41, Nathan Dunn <nd...@gm...> a écrit :

>
> I think you would either do this to search from within the jbrowse
> directory for non-annotated genes:
>
> https://jbrowse.org/docs/generate-names.pl.html
>
> For annotated genes, there should be a gene search box in the annotator
> panel at right under the annotations tab:
>
>
> https://genomearchitect.readthedocs.io/en/latest/UsersGuide.html#the-apollo-main-window
>
>
> Nathan
>
>
> On Apr 8, 2022, at 8:45 AM, uguyet <ug...@gm...> wrote:
>
> Hello,
> I would like to know if it is possible to search by gene name in Apollo
> and if so, could you explain how to do it?
> Thank you in advance,
> Ulysse
>
> --
> To unsubscribe from this group and stop receiving emails from it, send an
> email to apo...@lb....
>
>
>
>

Re: [Gmod-ajax] [apollo] search by gene name

[Nathan D. <nd...@gm...>]

I think you would either do this to search from within the jbrowse directory for non-annotated genes:

https://jbrowse.org/docs/generate-names.pl.html <https://jbrowse.org/docs/generate-names.pl.html>

For annotated genes, there should be a gene search box in the annotator panel at right under the annotations tab: 

https://genomearchitect.readthedocs.io/en/latest/UsersGuide.html#the-apollo-main-window <https://genomearchitect.readthedocs.io/en/latest/UsersGuide.html#the-apollo-main-window>


Nathan


> On Apr 8, 2022, at 8:45 AM, uguyet <ug...@gm...> wrote:
> 
> Hello,
> I would like to know if it is possible to search by gene name in Apollo and if so, could you explain how to do it?
> Thank you in advance,
> Ulysse
> 
> -- 
> To unsubscribe from this group and stop receiving emails from it, send an email to apo...@lb... <mailto:apo...@lb...>.

Re: [Gmod-ajax] A question for JBrowse1

[<fa...@ca...>]

Dear everyone,
    We have another question.  For the Alignments2 of reads alignments,  in a specified window,  we want to re-order the reads on the Y-axis orientation based on the sequence characteristcs.   For example, based on the sequence identity between each reads and reference genome.  The reads with the highest identity value will be displayed on the top， and the reads with the lowest identity value will be displayed on the bottom.  This display mode will help us developing a new functional genomic tool.

    Then,  what should we do?  We learned that JBrowse1 used perl in the server side, and javascript in the client side,  and we found a file in the source codes src/JBrowse/View/Track/Alignments2.js that is possibly responsible for drawing the Alignments2 figure.  Can we achieve our purpose by just modifying the javascript codes in this file Alignments2.js ？ Or any other code files needed to be modified?  Or should we write a plugin? 

    Looking forward to hearing from you!

Best regards,
Wei


fa...@ca...
 
From: fa...@ca...
Date: 2022-03-27 16:46
To: Colin; Scott Cain
CC: ihholmes; gmod-ajax
Subject: Re: Re: [Gmod-ajax] A question for JBrowse1
Thanks very much.   We have tested view->trackPadding, yes, it works now!  




fa...@ca...
 
From: Colin
Date: 2022-03-26 00:15
To: Scott Cain
CC: Ian Holmes; fa...@ca...; gmod-ajax
Subject: Re: [Gmod-ajax] A question for JBrowse1
>However, we met a problem on setting the distance between each tracks. 

You can try setting view->trackPadding (see   https://jbrowse.org/docs/global_options.html)


Basically, editing jbrowse.conf to have

[GENERAL]
view.trackPadding=0

-Colin


On Thu, Mar 24, 2022 at 3:08 PM Scott Cain <sc...@sc...> wrote:
Hi Wei,

While I agree with Ian's suggestion that you try JBrowse 2, if there is a reason you want to stick with JBrowse 1 for the moment, note that there is at least an option to add a little bit of space between tracks so that the labels don't overlap the features by adding "trackLabels = no-block" to the "[GENERAL]" section of the jbrowse.conf file for the entire site.

Scott


On Thu, Mar 24, 2022 at 1:48 PM Ian Holmes <ihh...@gm...> wrote:
Dear Wei,

Thanks for your interest in JBrowse. I'm glad it's been helpful to you!

JBrowse1, which is now in maintenance mode only, does not allow adjustment of the vertical height of tracks.
Active development of JBrowse is now focused on JBrowse2, whose "Linear Genome Browser" component reproduces most of the functionality of JBrowse1, while fixing a lot of the limitations. For example, it is easy to adjust the height of tracks in JBrowse2. There are also many new features, such as the ability to view synteny between genomes.
Furthermore, JBrowse2 should be straightforward to install on any website where you already have JBrowse1 installed.
We would be very interested in hearing feedback on your experience with JBrowse2, as we are actively encouraging new users to try JBrowse2, and would like to try and make the experience as easy as possible for you.

I have CC'd the JBrowse mailing list on this reply; you can also often get quicker responses by engaging with the software development team directly in the various ways described on the contact page on the JBrowse website.

Thanks & best wishes,
Ian

On Thu, Mar 24, 2022 at 4:00 AM fa...@ca... <fa...@ca...> wrote:
Dear Prof. Holmes,
      We are trying to build a genome website for our sequenced species, and found JBrowse1 an excellent tool to use.   However, we met a problem on setting the distance between each tracks.  Is there a way to set the distance of drawing among any neiboring tracks? 
     Thanks for your great work.  I am looking forward to hearing from you! 

Wei Fan
Agriculture genomics Institute at Shenzhen, China


fa...@ca...
_______________________________________________
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/)
_______________________________________________
Gmod-ajax mailing list
Gmo...@li...
https://lists.sourceforge.net/lists/listinfo/gmod-ajax