gmod-ajax — JBrowse list

Re: [Gmod-ajax] can not load bam file

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

Hi Julia,

At first, I thought the colon ":" in the reference sequence name was going
to cause a problem, but it appears to work (Colin told me it worked for
him).  Usually when you open the javascript console, you'll get the error
console by default, so I would guess that's what you saw. If you want to
send a screenshot to make sure, that would be fine.

Finally, if you want to/can, you are welcome to send the sequence and bam
files to me individually and I can try to see if I can sort out what's
going on.

Scott



On Tue, Jun 2, 2020 at 1:24 AM Zieringer, Julia <
jul...@ib...> wrote:

> Hi Scott,
>
>
>
> there is nothing showing up when i open the bam and bai file. I checked
> the name oft he reference sequence and it is the same in the bam file, as
> far as i can tell…
>
> Reference file:
>
> Corresponding Bam file:
>
>
>
>
>
> I used the debug tool in the desktop app (unfortunately Jbrowse is not
> available on our galaxy server yet) to see if an error message is showing
> up in the console, but nothing happened here. However i am not sure if i
> look at the right part of the debuger? I am not familiar with this tool.
>
>
>
> Thanks a lot for your help,
>
> Julia
>
>
>
>
>
>
>
>
>
> *Von:* Scott Cain [mailto:sc...@sc...]
> *Gesendet:* Freitag, 29. Mai 2020 20:27
> *An:* Zieringer, Julia <jul...@ib...>
> *Cc:* gmo...@li...
> *Betreff:* Re: [Gmod-ajax] can not load bam file
>
>
>
> Hi Julia,
>
>
>
> Did the track show up but it was empty? If so, my first guess would be
> that the name of the reference sequence in the BAM file doesn't agree with
> the name of the reference sequence in the rest of JBrowse.  If that's not
> what's going on, can you open up the browser's javascript console (under
> View in chrome, under Developer in Safari and under Tools in Firefox) and
> see if there are any error messages that might point to what the problem is?
>
>
>
> If it's available on a public server, if you could give us the url (via
> private email if necessary) we can take a look to see if we can figure it
> out.
>
>
>
> Scott
>
>
>
>
>
> On Fri, May 29, 2020 at 11:09 AM Zieringer, Julia <
> jul...@ib...> wrote:
>
> Hello,
>
>
>
> my name is Julia and I am from Germany. I used snippy on a Galaxy server
> to identify variants between two genomes. Ti visualize the variants and
> coverage I want to import the fasta sequence file of my reference, the
> variants from the gff3 and the bam file to see the alignments in the
> desktop app of JBrowse. I can import the sequence fasta file of my
> reference and the corresponding gff3 file with the variants without a
> problem, however as soon as i want to load the bam (and Bam index file bai)
> it is not working.
>
>
>
> I go to track (ater i loaded the genome sequence) and load both, the bam
> and bai file. Afterwards i simply click open and the import-window
> disapears but nothing is showing up?! I do not know what is going on… or if
> something is missing?
>
>
>
> Thank you very much,
>
> Julia
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
>
> --
>
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

Re: [Gmod-ajax] [apollo] Command to display marker track in Apollo

[Nathan D. <nat...@lb...>]

Abhjit, 

I am going to expand this to the JBrowse general mailing list as this is more of a JBrowse question. 

I’ve never actually tried to do this specifically.  

If for some reason you get this to work in JBrowse, but not Apollo, please let me know. 

Nathan



> On Jun 2, 2020, at 6:59 AM, Abhijit Sanyal <abh...@gm...> wrote:
> 
> Hello All,
> 
> I would like to display markers on Apollo as tracks. I am still a novice in using Apollo, so still learning the basics. I have the following command for displaying gene tracks
> 
> /app/Apollo/bin/flatfile-to-json.pl --gff /Apollo-TEMP/displayname.gff3 --arrowheadClass trellis-arrowhead --subfeatureClasses '{"CDS":"pink-90pct", "five_prime_UTR":"purple-60pct", "three_prime_UTR":"purple-60pct", "exon":"container-100pct"}' --className container-16px --type mRNA --trackLabel Gene-Models --out /apollo-annotation/genome/maize/Annot1/data/
> 
> I would like to modify that to display SNP markers as arrowheads or little triangles, and other genetic markers as rectangles, both magenta in colour. I have gotten as far as below. Need a little help modifying the rest of the code.
> 
> /app/Apollo/bin/flatfile-to-json.pl --gff /Apollo-TEMP/gsap645_markers.gff3 --arrowheadClass trellis-arrowhead --className ?? --type genetic_marker --key blast --subfeatureClasses '{"??"}' --trackLabel GENETIC-MARKER --out /apollo-annotation/genome/maize/Annot1/data/
> 
> The "??" are the places where I do not know what value to put, in order to get the desired effect of triangle or a rectangle. Also I do not know where to specify the color. Thank you for your help
> 
> -Abhijit
> 

Re: [Gmod-ajax] can not load bam file

[Zieringer, J. <jul...@ib...>]

Hi Scott,

there is nothing showing up when i open the bam and bai file. I checked the name oft he reference sequence and it is the same in the bam file, as far as i can tell…
Reference file:
[cid:image001.png@01D638C7.F844BCB0]
Corresponding Bam file:
[cid:image002.png@01D638C7.F844BCB0]


I used the debug tool in the desktop app (unfortunately Jbrowse is not available on our galaxy server yet) to see if an error message is showing up in the console, but nothing happened here. However i am not sure if i look at the right part of the debuger? I am not familiar with this tool.

Thanks a lot for your help,
Julia




Von: Scott Cain [mailto:sc...@sc...]
Gesendet: Freitag, 29. Mai 2020 20:27
An: Zieringer, Julia <jul...@ib...>
Cc: gmo...@li...
Betreff: Re: [Gmod-ajax] can not load bam file

Hi Julia,

Did the track show up but it was empty? If so, my first guess would be that the name of the reference sequence in the BAM file doesn't agree with the name of the reference sequence in the rest of JBrowse.  If that's not what's going on, can you open up the browser's javascript console (under View in chrome, under Developer in Safari and under Tools in Firefox) and see if there are any error messages that might point to what the problem is?

If it's available on a public server, if you could give us the url (via private email if necessary) we can take a look to see if we can figure it out.

Scott


On Fri, May 29, 2020 at 11:09 AM Zieringer, Julia <jul...@ib...<mailto:jul...@ib...>> wrote:
Hello,

my name is Julia and I am from Germany. I used snippy on a Galaxy server to identify variants between two genomes. Ti visualize the variants and coverage I want to import the fasta sequence file of my reference, the variants from the gff3 and the bam file to see the alignments in the desktop app of JBrowse. I can import the sequence fasta file of my reference and the corresponding gff3 file with the variants without a problem, however as soon as i want to load the bam (and Bam index file bai) it is not working.

I go to track (ater i loaded the genome sequence) and load both, the bam and bai file. Afterwards i simply click open and the import-window disapears but nothing is showing up?! I do not know what is going on… or if something is missing?

Thank you very much,
Julia
_______________________________________________
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 Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

Re: [Gmod-ajax] can not load bam file

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

Hi Julia,

Did the track show up but it was empty? If so, my first guess would be that
the name of the reference sequence in the BAM file doesn't agree with the
name of the reference sequence in the rest of JBrowse.  If that's not
what's going on, can you open up the browser's javascript console (under
View in chrome, under Developer in Safari and under Tools in Firefox) and
see if there are any error messages that might point to what the problem is?

If it's available on a public server, if you could give us the url (via
private email if necessary) we can take a look to see if we can figure it
out.

Scott


On Fri, May 29, 2020 at 11:09 AM Zieringer, Julia <
jul...@ib...> wrote:

> Hello,
>
>
>
> my name is Julia and I am from Germany. I used snippy on a Galaxy server
> to identify variants between two genomes. Ti visualize the variants and
> coverage I want to import the fasta sequence file of my reference, the
> variants from the gff3 and the bam file to see the alignments in the
> desktop app of JBrowse. I can import the sequence fasta file of my
> reference and the corresponding gff3 file with the variants without a
> problem, however as soon as i want to load the bam (and Bam index file bai)
> it is not working.
>
>
>
> I go to track (ater i loaded the genome sequence) and load both, the bam
> and bai file. Afterwards i simply click open and the import-window
> disapears but nothing is showing up?! I do not know what is going on… or if
> something is missing?
>
>
>
> Thank you very much,
>
> Julia
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

[Gmod-ajax] can not load bam file

[Zieringer, J. <jul...@ib...>]

Hello,

my name is Julia and I am from Germany. I used snippy on a Galaxy server to identify variants between two genomes. Ti visualize the variants and coverage I want to import the fasta sequence file of my reference, the variants from the gff3 and the bam file to see the alignments in the desktop app of JBrowse. I can import the sequence fasta file of my reference and the corresponding gff3 file with the variants without a problem, however as soon as i want to load the bam (and Bam index file bai) it is not working.

I go to track (ater i loaded the genome sequence) and load both, the bam and bai file. Afterwards i simply click open and the import-window disapears but nothing is showing up?! I do not know what is going on... or if something is missing?

Thank you very much,
Julia

[Gmod-ajax] JBrowse 1.16.9 maintenance release

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

Hi all! I am pleased to announce the release of JBrowse 1.16.9

This contains a couple small bugfixes and features and includes great
feedback from the community. Thanks to our users, issue creators, and PR
submitters!

   - JBrowse-1.16.9.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.9-release/JBrowse-1.16.9.zip>
-
   minified release
   - JBrowse-1.16.9-dev.zip
   <https://github.com/GMOD/jbrowse/archive/1.16.9-release.zip> - use this
   if you modify jbrowse source code or use plugins
   - JBrowse-1.16.9-desktop-win32-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.9-release/JBrowse-1.16.9-desktop-win32-x64.zip>
   - JBrowse-1.16.9-desktop-linux-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.9-release/JBrowse-1.16.9-desktop-linux-x64.zip>
   - JBrowse-1.16.9-desktop-darwin-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.9-release/JBrowse-1.16.9-desktop-darwin-x64.zip>


Blog post http://jbrowse.org/blog/2020/05/21/jbrowse-1-16-9.html
<http://jbrowse.org/blog/#minor-improvements>Minor improvements

   -

   Added a 'Reset to defaults' menu item, which addresses a long standing
   issue. Thanks to a user with a very long github name for their contribution
   (issue #1496 <https://github.com/gmod/jbrowse/pull/1496>, issue #764
   <https://github.com/gmod/jbrowse/issues/764>).
   -

   Disable coordinate indicator on tab switch, thanks @lukaw3d
   <https://github.com/lukaw3d> (issue #1497
   <https://github.com/gmod/jbrowse/pull/1497>)
   -

   Small optimization bumping @gmod <https://github.com/gmod>/bam from
   version 1.0.35->1.0.36 (@cmdcolin <https://github.com/cmdcolin>)
   -

   Add ability to include/hide variant filters instead of just hide (
   @cmdcolin <https://github.com/cmdcolin>, issue #1478
   <https://github.com/gmod/jbrowse/issues/1478>)
   -

   Add ability to color by TS tag. The useXS config now applies to XS and TS,
   and the useTS tag only applies to the lower-case ts tag used by minimap2
   (issue #1493 <https://github.com/gmod/jbrowse/pull/1493>, @cmdcolin
   <https://github.com/cmdcolin>)

<http://jbrowse.org/blog/#bug-fixes>Bug fixes

   -

   Fixed a race condition in the http-range-fetcher module that caused
   "Error: "failed to retrieve file size"" messages when many tracks were
   opened at once. Thanks to @russellmyers
<https://github.com/russellmyers> for
   the bug report! (issue #1473
   <https://github.com/gmod/jbrowse/issues/1473>)
   -

   Fixed error with exporting highlighted regions with Save track data,
   thanks to @lipan6461188 <https://github.com/lipan6461188> for
reporting (issue
   #1488 <https://github.com/gmod/jbrowse/issues/1488>)
   -

   Fixed ability to have custom mouseovers on features that have no default
   mouseover e.g. features with no name or ID. Thanks to @scottcain
   <https://github.com/scottcain> for reporting (issue #1487
   <https://github.com/gmod/jbrowse/pull/1487>)
   -

   Fixed the response for requests to HTTP 403 errors. Thanks to
   @ilaydabozan <https://github.com/ilaydabozan> for reporting (issue #1490
   <https://github.com/gmod/jbrowse/issues/1490>)
   -

   When there is only a single coordinate column in a tabix file, there is
   now improved performance since the overlap checking code was incorrect
   before in @gmod <https://github.com/gmod>/tabix (@cmdcolin
   <https://github.com/cmdcolin>)
   -

   Fix usage of bigwig "scoreType":"maxScore" config for bigwig tracks (
   @cmdcolin <https://github.com/cmdcolin>, issue #1380
   <https://github.com/gmod/jbrowse/issues/1380>)
   -

   Fix a crash related to NCList histogram when a featureScale is
applied (issue
   #1327 <https://github.com/gmod/jbrowse/issues/1327>)
   -

   Make it so that VCF tracks don't require CORS headers for Content-Range (
   @cmdcolin <https://github.com/cmdcolin>)


-Colin

[Gmod-ajax] Apollo 2.6.0 Released

[Nathan D. <nat...@lb...>]

Apollo 2.6.0 has been released: https://github.com/GMOD/Apollo/releases/tag/2.6.0 <https://github.com/GMOD/Apollo/releases/tag/2.6.0>

Major features include:

Removed popups for annotations in favor of annotator panel tabs 2334 <https://github.com/GMOD/Apollo/pull/2334>
Implemented gene product and field provenance annotations with evidence and GFF3 export 2371 <https://github.com/GMOD/Apollo/pull/2371>, 2234 <https://github.com/GMOD/Apollo/pull/2234>, 2312 <https://github.com/GMOD/Apollo/pull/2312>, 2424 <https://github.com/GMOD/Apollo/pull/2424>
Added GO Annotations to GFF3 export and extended to transcript 2400 <https://github.com/GMOD/Apollo/pull/2400>
loadLink can take name of gene in evidence (if JBrowse names have been processed) 2444 <https://github.com/GMOD/Apollo/pull/2444>
Add alias to user interface and GFF3 export 2277 <https://github.com/GMOD/Apollo/pull/2277>
Split out default GO Evidence Codes from ECO codes 2429 <https://github.com/GMOD/Apollo/pull/2429>

There are numerous other features, bug fixes and infrastructure changes as well.
More changes can be found here: https://github.com/GMOD/Apollo/blob/develop/ChangeLog.md <https://github.com/GMOD/Apollo/blob/develop/ChangeLog.md>
Docker builds are on quay.io and docker hub:

https://quay.io/repository/gmod/apollo?tab=builds <https://quay.io/repository/gmod/apollo?tab=builds>
https://hub.docker.com/r/gmod/apollo <https://hub.docker.com/r/gmod/apollo>
Please review the documentation pages for more details: http://genomearchitect.readthedocs.io/en/latest/ <http://genomearchitect.readthedocs.io/en/latest/>
Note: You can find a guide upgrading existing Apollo installations here:
https://genomearchitect.readthedocs.io/en/latest/Migration.html <https://genomearchitect.readthedocs.io/en/latest/Migration.html>
Report issues <https://github.com/GMOD/Apollo/issues> if found to GitHub: https://github.com/GMOD/Apollo/issues


Active mailing list (ap...@lb... <mailto:ap...@lb...>) and the google group: https://groups.google.com/a/lbl.gov/forum/#!forum/apollo

AWS EC2 Community images of Apollo 2.6.0 will be available within the N. Virginia and California regions minimally. Please request on the forum or ticketing system if more are needed.


Cheers,

The Apollo Team

Re: [Gmod-ajax] jbrowse issue

[sergio c. <con...@gm...>]

thank you colin, i did not have time to check the refseq issue yet, but
your answers clearly point to the issue and i hope to check this soon.
thanks!
sergio

On Mon, Apr 27, 2020 at 9:40 PM Colin <col...@gm...> wrote:

> Hi there,
>
> Were there any updates here? I think that Scott Cain pointed out basically
> the important thing which was that refSeqs.json is not loading. It is ok
> for tracks.conf not to load (it is just an extra type of configuration,
> just the same stuff that can be in trackList.json but in a different syntax)
>
> For flymine it looks like refSeqs.json loads ok, at this jbrowse URL:
>
>
> http://jbrowse.intermine.org/?data=https%3A%2F%2Fwww.flymine.org%2Fquery%2Fservice%2Fjbrowse%2Fconfig%2F7227&loc=2L%3A9405770..14108511&tracks=&highlight=
>
>
> It loads this refSeqs.json:
> https://www.flymine.org/query/service/jbrowse/config/7227/seq/refSeqs.json
>
> But for covidmine it looks for this refSeqs.json:
> https://test.intermine.org/covidmine/service/jbrowse/config/2697049/seq/refSeqs.json
>
> Which gives a 404
>
> -Colin
>
>
> On Fri, Apr 24, 2020 at 1:43 PM Scott Cain <sc...@sc...> wrote:
>
>> Hi Sergio,
>>
>> Does tracks.conf exist? JBrowse does complain if it doesn't get it, but
>> it doesn't care if it's empty, so a `touch tracks.conf` may do the trick.
>> The 404 on refSeqs.json is also a pretty big problem; is it present in the
>> seq directory?
>>
>> Scott
>>
>>
>> On Fri, Apr 24, 2020 at 9:37 AM <con...@in...> wrote:
>>
>>> dear jbrowse team,
>>> i have various (intermine) applications using jbrowse, but i cannot make
>>> one working (from the same jbrowse server).
>>> i attach a screenshot which should illustrate the problem: the
>>> tracks.conf is not beind served (trackList et al seems ok).
>>> i'm using JBrowse-1.16.6, and the setup for the various mine is
>>> hopefully the same.
>>> i'm wondering if it can be a data issue?
>>> any help/pointer would be great!
>>> thanks
>>> sergio
>>>
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

-- 
sergiocontrino.github.io      betterthantv.co.uk      FOLLOW on Spotify
<https://open.spotify.com/artist/5ADQWx1XOm5YwENg7ioBWO>

Re: [Gmod-ajax] jbrowse issue

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

Hi there,

Were there any updates here? I think that Scott Cain pointed out basically
the important thing which was that refSeqs.json is not loading. It is ok
for tracks.conf not to load (it is just an extra type of configuration,
just the same stuff that can be in trackList.json but in a different syntax)

For flymine it looks like refSeqs.json loads ok, at this jbrowse URL:

http://jbrowse.intermine.org/?data=https%3A%2F%2Fwww.flymine.org%2Fquery%2Fservice%2Fjbrowse%2Fconfig%2F7227&loc=2L%3A9405770..14108511&tracks=&highlight=


It loads this refSeqs.json:
https://www.flymine.org/query/service/jbrowse/config/7227/seq/refSeqs.json

But for covidmine it looks for this refSeqs.json:
https://test.intermine.org/covidmine/service/jbrowse/config/2697049/seq/refSeqs.json

Which gives a 404

-Colin


On Fri, Apr 24, 2020 at 1:43 PM Scott Cain <sc...@sc...> wrote:

> Hi Sergio,
>
> Does tracks.conf exist? JBrowse does complain if it doesn't get it, but it
> doesn't care if it's empty, so a `touch tracks.conf` may do the trick. The
> 404 on refSeqs.json is also a pretty big problem; is it present in the seq
> directory?
>
> Scott
>
>
> On Fri, Apr 24, 2020 at 9:37 AM <con...@in...> wrote:
>
>> dear jbrowse team,
>> i have various (intermine) applications using jbrowse, but i cannot make
>> one working (from the same jbrowse server).
>> i attach a screenshot which should illustrate the problem: the
>> tracks.conf is not beind served (trackList et al seems ok).
>> i'm using JBrowse-1.16.6, and the setup for the various mine is
>> hopefully the same.
>> i'm wondering if it can be a data issue?
>> any help/pointer would be great!
>> thanks
>> sergio
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] jbrowse issue

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

Hi Sergio,

Does tracks.conf exist? JBrowse does complain if it doesn't get it, but it
doesn't care if it's empty, so a `touch tracks.conf` may do the trick. The
404 on refSeqs.json is also a pretty big problem; is it present in the seq
directory?

Scott


On Fri, Apr 24, 2020 at 9:37 AM <con...@in...> wrote:

> dear jbrowse team,
> i have various (intermine) applications using jbrowse, but i cannot make
> one working (from the same jbrowse server).
> i attach a screenshot which should illustrate the problem: the
> tracks.conf is not beind served (trackList et al seems ok).
> i'm using JBrowse-1.16.6, and the setup for the various mine is
> hopefully the same.
> i'm wondering if it can be a data issue?
> any help/pointer would be great!
> thanks
> sergio
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

[Gmod-ajax] jbrowse issue

[<con...@in...>]

dear jbrowse team,
i have various (intermine) applications using jbrowse, but i cannot make 
one working (from the same jbrowse server).
i attach a screenshot which should illustrate the problem: the 
tracks.conf is not beind served (trackList et al seems ok).
i'm using JBrowse-1.16.6, and the setup for the various mine is 
hopefully the same.
i'm wondering if it can be a data issue?
any help/pointer would be great!
thanks
sergio

Re: [Gmod-ajax] COVID-19 Apollo docker

[Nathan D. <nat...@lb...>]

I just wanted to say that we have an update for the Apollo server.

http://covid19apollo.jbrowse.org/annotator/index <http://covid19apollo.jbrowse.org/annotator/index> with username and password:

demouser / demo1234

with updated JBrowse data from http://covid19.jbrowse.org/ <http://covid19.jbrowse.org/>

If you want to run your own docker image, we have instructions here:

https://hub.docker.com/repository/docker/gmod/sars-cov-2-apollo <https://hub.docker.com/repository/docker/gmod/sars-cov-2-apollo>

Have a safe and relaxing weekend all,

Nathan


> On Mar 17, 2020, at 3:44 PM, Nathan Dunn <nat...@lb...> wrote:
> 
> 
> Scott Cain had put together a nice COVID-19 JBrowse docker image here:
> 
> https://hub.docker.com/repository/docker/gmod/sars-cov-2-jbrowse <https://hub.docker.com/repository/docker/gmod/sars-cov-2-jbrowse>
> 
> Its running on a server for now here:
> 
> http://covid19.jbrowse.org/jbrowse/ <http://covid19.jbrowse.org/jbrowse/>
> 
> 
> I’ve integrated this into an Apollo docker image here:
> 
> https://hub.docker.com/repository/docker/gmod/sars-cov-2-apollo <https://hub.docker.com/repository/docker/gmod/sars-cov-2-apollo>
> 
> If you wan tot play with it, It is running here: http://covid19apollo.jbrowse.org/annotator/index <http://covid19apollo.jbrowse.org/annotator/index> with username de...@de... <mailto:de...@de...> / demo , or admin@local.host <mailto:admin@local.host> / demo 
> 
> Obviously this server is insecure, so don’t put up anything you don’t want other folks to see. 
> 
> This installs a few custom plugins, so may not be as easy as adding the data directly (though copying and pasting the track data should work).
> 
> Please let me know if you have any questions. 
> 
> Nathan

Re: [Gmod-ajax] disabling to download data

[Nathan D. <nat...@lb...>]

If you are talking about downloaded via annotated tracks in Apollo, I updated the permissions so that users need minimally “export” permissions to export.  We have kind of left this loose. 

I still need update error reporting: https://github.com/GMOD/Apollo/issues/2431 <https://github.com/GMOD/Apollo/issues/2431>

That being said, if users can write, they can also export.  This is necessary as annotators (with write permission) will need to be able to inspect their annotations as GFF3.



Nathan


> On Apr 8, 2020, at 4:41 AM, Mic <mic...@gm...> wrote:
> 
> Hi,
> Is there a way to download in JBrowser/Apollo the whole genome assembly and annotation. If yes then is there a way to block the download of it?
> 
> Thank you in advance
> 
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

[Gmod-ajax] disabling to download data

[Mic <mic...@gm...>]

Hi,
Is there a way to download in JBrowser/Apollo the whole genome assembly and
annotation. If yes then is there a way to block the download of it?

Thank you in advance

Re: [Gmod-ajax] JBrower download is very slow

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

Hello,

Sorry, I tried to send it via email but Google wouldn't allow the
attachment--it looks too suspicious to them.  If you have any other
alternatives, please let me know.

Scott


On Tue, Mar 24, 2020 at 1:07 PM Scott Cain <sc...@sc...> wrote:

> Hello,
>
> The developer release file is about 14 MB, which is a little big for
> email.  I'll try to send it to you, but it may not go through.  I'll send
> it off list so everybody on this list doesn't get a copy in their mail box.
>
> Scott
>
>
> On Tue, Mar 24, 2020 at 1:04 PM 周秉博 <152...@16...> wrote:
>
>> JBrower download is very slow,please send to me the new version  to my
>> email!
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

Re: [Gmod-ajax] JBrower download is very slow

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

Hello,

The developer release file is about 14 MB, which is a little big for
email.  I'll try to send it to you, but it may not go through.  I'll send
it off list so everybody on this list doesn't get a copy in their mail box.

Scott


On Tue, Mar 24, 2020 at 1:04 PM 周秉博 <152...@16...> wrote:

> JBrower download is very slow,please send to me the new version  to my
> email!
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

[Gmod-ajax] JBrower download is very slow

[周秉博 <152...@16...>]

JBrower download is very slow,please send to me the new version  to my email!











|
|
|

[Gmod-ajax] COVID-19 Apollo docker

[Nathan D. <nat...@lb...>]

Scott Cain had put together a nice COVID-19 JBrowse docker image here:

https://hub.docker.com/repository/docker/gmod/sars-cov-2-jbrowse <https://hub.docker.com/repository/docker/gmod/sars-cov-2-jbrowse>

Its running on a server for now here:

http://covid19.jbrowse.org/jbrowse/ <http://covid19.jbrowse.org/jbrowse/>


I’ve integrated this into an Apollo docker image here:

https://hub.docker.com/repository/docker/gmod/sars-cov-2-apollo <https://hub.docker.com/repository/docker/gmod/sars-cov-2-apollo>

If you wan tot play with it, It is running here: http://covid19apollo.jbrowse.org/annotator/index <http://covid19apollo.jbrowse.org/annotator/index> with username de...@de... / demo , or admin@local.host / demo 

Obviously this server is insecure, so don’t put up anything you don’t want other folks to see. 

This installs a few custom plugins, so may not be as easy as adding the data directly (though copying and pasting the track data should work).

Please let me know if you have any questions. 

Nathan

Re: [Gmod-ajax] Problem loading jbrowse page

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

Yes, that is certainly a local networking issue. You’ll have to ask them to open port 80 if you want it widely available, or help you with ssh tunneling if it’s just for you. Good luck!

Scott


> On Mar 13, 2020, at 4:06 AM, Katerina Pa <kat...@gm...> wrote:
> 
> 
> Dear Scott,
> 
> I am getting the same error for http://ip.address./index.html so I guess its a networking problem. The host machine (server) is in the building with all university servers and in order to access it through putty, I have to use the wire connection when  in the university or the wifi with the university vpn client. So I should ask help from the people here in the uni?
> Thank you in any case for your time and effort!
> 
> Cheers,
> /Katerina
> 
>> On Thu, Mar 12, 2020 at 5:33 PM Scott Cain <sc...@sc...> wrote:
>> Hi Katerina,
>> 
>> Please reply all so that other people on the list can jump in and help.  It sounds like you're doing the right things.  If you point your browser at http://ipaddress/index.html, you should get a generic "apache is working" sort of page.  If you don't see that, you have a networking problem that I may not be able to help you with.  Where is the host machine?
>> 
>> Scott
>> 
>> 
>>> On Thu, Mar 12, 2020 at 3:32 AM Katerina Pa <kat...@gm...> wrote:
>>> Dear Scott,
>>> 
>>> Thank you for replying so quickly.
>>> 
>>> 1. /etc/init.d/apache2 restart
>>> [ ok ] Restarting apache2 (via systemctl): apache2.service.
>>> 
>>> So I guess this is not the problem.
>>> 
>>> 2. JBrowse is in /var/www/jbrowse but i also have tried with /var/www/html/jbrowse and I get the same error.
>>> 
>>> 3. As IP address I use the one that I also use in Host in Putty to connect to our server. When I run jconfig it is the one found in
>>> eno1      Link encap:Ethernet 
>>>           inet addr: .....
>>> 
>>> Is that the right address?
>>> 
>>> Cheers,
>>> /Katerina
>>> 
>>> 
>>> 
>>>> On Tue, Mar 10, 2020 at 6:08 PM Scott Cain <sc...@sc...> wrote:
>>>> Hi Katerina,
>>>> 
>>>> A few things to check:
>>>> 
>>>> 1. Is apache actually running? Try 'sudo /etc/init.d/apache2 restart' and see if the last line of the output starts with 'OK' (this seems like it's probably the problem)
>>>> 
>>>> 2. Is JBrowse in the right place? From your description, I would guess it's in /var/www/html/jbrowse but if not, I don't think you're using the right URL.
>>>> 
>>>> 3. Make sure the IP address is right.  Check the output of ifconfig.
>>>> 
>>>> Scott
>>>> 
>>>> 
>>>> 
>>>> 
>>>>> On Tue, Mar 10, 2020 at 10:04 AM Katerina Pa <kat...@gm...> wrote:
>>>>> Hello,
>>>>> 
>>>>> I have downloaded and installed jbrowse in /var/www running setup.sh.
>>>>> After installing some missing modules, everything was fine and I got the messages that volvox is ready to see online. But when I try to open 
>>>>> http://my.IP.address/jbrowse/index.html?data=sample_data/json/volvox
>>>>> or just
>>>>> http://my.IP.address/jbrowse/ 
>>>>> I get :
>>>>> 
>>>>> The connection has timed out
>>>>> 
>>>>> The server at xxx.xxx.xxx.xx is taking too long to respond.
>>>>> 
>>>>>     The site could be temporarily unavailable or too busy. Try again in a few moments.
>>>>>     If you are unable to load any pages, check your computer’s network connection.
>>>>>     If your computer or network is protected by a firewall or proxy, make sure that Firefox is permitted to access the Web.
>>>>> 
>>>>> I am not quite sure what the problem is.  Is it just that the server is too slow to respond or could it be sth else? I have installed jbrowse in  Ubuntu 16.04.6 LTS.
>>>>> There should also be apache available, since when I do
>>>>> which apache2
>>>>> I get
>>>>> /usr/sbin/apache2
>>>>> 
>>>>> Any hints on the issue here would be very helpful.
>>>>> Thank you in advance.
>>>>> 
>>>>> Kind regards,
>>>>> /Katerina
>>>>> 
>>>>> _______________________________________________
>>>>> Gmod-ajax mailing list
>>>>> Gmo...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>> 
>>>> 
>>>> -- 
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>> Ontario Institute for Cancer Research
>> 
>> 
>> -- 
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research

Re: [Gmod-ajax] Problem loading jbrowse page

[Katerina Pa <kat...@gm...>]

Dear Scott,

I am getting the same error for http://ip.address./index.html so I guess
its a networking problem. The host machine (server) is in the building with
all university servers and in order to access it through putty, I have to
use the wire connection when  in the university or the wifi with the
university vpn client. So I should ask help from the people here in the uni?
Thank you in any case for your time and effort!

Cheers,
/Katerina

On Thu, Mar 12, 2020 at 5:33 PM Scott Cain <sc...@sc...> wrote:

> Hi Katerina,
>
> Please reply all so that other people on the list can jump in and help.
> It sounds like you're doing the right things.  If you point your browser at
> http://ipaddress/index.html, you should get a generic "apache is working"
> sort of page.  If you don't see that, you have a networking problem that I
> may not be able to help you with.  Where is the host machine?
>
> Scott
>
>
> On Thu, Mar 12, 2020 at 3:32 AM Katerina Pa <kat...@gm...>
> wrote:
>
>> Dear Scott,
>>
>> Thank you for replying so quickly.
>>
>> 1. /etc/init.d/apache2 restart
>> [ ok ] Restarting apache2 (via systemctl): apache2.service.
>>
>> So I guess this is not the problem.
>>
>> 2. JBrowse is in /var/www/jbrowse but i also have tried with
>> /var/www/html/jbrowse and I get the same error.
>>
>> 3. As IP address I use the one that I also use in Host in Putty to
>> connect to our server. When I run jconfig it is the one found in
>> eno1      Link encap:Ethernet
>>           inet addr: .....
>>
>> Is that the right address?
>>
>> Cheers,
>> /Katerina
>>
>>
>>
>> On Tue, Mar 10, 2020 at 6:08 PM Scott Cain <sc...@sc...> wrote:
>>
>>> Hi Katerina,
>>>
>>> A few things to check:
>>>
>>> 1. Is apache actually running? Try 'sudo /etc/init.d/apache2 restart'
>>> and see if the last line of the output starts with 'OK' (this seems like
>>> it's probably the problem)
>>>
>>> 2. Is JBrowse in the right place? From your description, I would guess
>>> it's in /var/www/html/jbrowse but if not, I don't think you're using the
>>> right URL.
>>>
>>> 3. Make sure the IP address is right.  Check the output of ifconfig.
>>>
>>> Scott
>>>
>>>
>>>
>>>
>>> On Tue, Mar 10, 2020 at 10:04 AM Katerina Pa <kat...@gm...>
>>> wrote:
>>>
>>>> Hello,
>>>>
>>>> I have downloaded and installed jbrowse in /var/www running setup.sh.
>>>> After installing some missing modules, everything was fine and I got
>>>> the messages that volvox is ready to see online. But when I try to open
>>>> http://my.IP.address/jbrowse/index.html?data=sample_data/json/volvox
>>>> <http://157.193.228.78/jbrowse/index.html?data=sample_data/json/volvox>
>>>> or just
>>>> http://my.IP.address/jbrowse/
>>>> I get :
>>>>
>>>> The connection has timed out
>>>>
>>>> The server at xxx.xxx.xxx.xx is taking too long to respond.
>>>>
>>>>     The site could be temporarily unavailable or too busy. Try again in
>>>> a few moments.
>>>>     If you are unable to load any pages, check your computer’s network
>>>> connection.
>>>>     If your computer or network is protected by a firewall or proxy,
>>>> make sure that Firefox is permitted to access the Web.
>>>>
>>>> I am not quite sure what the problem is.  Is it just that the server is
>>>> too slow to respond or could it be sth else? I have installed jbrowse in
>>>> Ubuntu 16.04.6 LTS.
>>>> There should also be apache available, since when I do
>>>> which apache2
>>>> I get
>>>> /usr/sbin/apache2
>>>>
>>>> Any hints on the issue here would be very helpful.
>>>> Thank you in advance.
>>>>
>>>> Kind regards,
>>>> /Katerina
>>>>
>>>> _______________________________________________
>>>> Gmod-ajax mailing list
>>>> Gmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain
>>> dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>>
>>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>

Re: [Gmod-ajax] Problem loading jbrowse page

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

Hi Katerina,

Please reply all so that other people on the list can jump in and help.  It
sounds like you're doing the right things.  If you point your browser at
http://ipaddress/index.html, you should get a generic "apache is working"
sort of page.  If you don't see that, you have a networking problem that I
may not be able to help you with.  Where is the host machine?

Scott


On Thu, Mar 12, 2020 at 3:32 AM Katerina Pa <kat...@gm...>
wrote:

> Dear Scott,
>
> Thank you for replying so quickly.
>
> 1. /etc/init.d/apache2 restart
> [ ok ] Restarting apache2 (via systemctl): apache2.service.
>
> So I guess this is not the problem.
>
> 2. JBrowse is in /var/www/jbrowse but i also have tried with
> /var/www/html/jbrowse and I get the same error.
>
> 3. As IP address I use the one that I also use in Host in Putty to connect
> to our server. When I run jconfig it is the one found in
> eno1      Link encap:Ethernet
>           inet addr: .....
>
> Is that the right address?
>
> Cheers,
> /Katerina
>
>
>
> On Tue, Mar 10, 2020 at 6:08 PM Scott Cain <sc...@sc...> wrote:
>
>> Hi Katerina,
>>
>> A few things to check:
>>
>> 1. Is apache actually running? Try 'sudo /etc/init.d/apache2 restart' and
>> see if the last line of the output starts with 'OK' (this seems like it's
>> probably the problem)
>>
>> 2. Is JBrowse in the right place? From your description, I would guess
>> it's in /var/www/html/jbrowse but if not, I don't think you're using the
>> right URL.
>>
>> 3. Make sure the IP address is right.  Check the output of ifconfig.
>>
>> Scott
>>
>>
>>
>>
>> On Tue, Mar 10, 2020 at 10:04 AM Katerina Pa <kat...@gm...>
>> wrote:
>>
>>> Hello,
>>>
>>> I have downloaded and installed jbrowse in /var/www running setup.sh.
>>> After installing some missing modules, everything was fine and I got the
>>> messages that volvox is ready to see online. But when I try to open
>>> http://my.IP.address/jbrowse/index.html?data=sample_data/json/volvox
>>> <http://157.193.228.78/jbrowse/index.html?data=sample_data/json/volvox>
>>> or just
>>> http://my.IP.address/jbrowse/
>>> I get :
>>>
>>> The connection has timed out
>>>
>>> The server at xxx.xxx.xxx.xx is taking too long to respond.
>>>
>>>     The site could be temporarily unavailable or too busy. Try again in
>>> a few moments.
>>>     If you are unable to load any pages, check your computer’s network
>>> connection.
>>>     If your computer or network is protected by a firewall or proxy,
>>> make sure that Firefox is permitted to access the Web.
>>>
>>> I am not quite sure what the problem is.  Is it just that the server is
>>> too slow to respond or could it be sth else? I have installed jbrowse in
>>> Ubuntu 16.04.6 LTS.
>>> There should also be apache available, since when I do
>>> which apache2
>>> I get
>>> /usr/sbin/apache2
>>>
>>> Any hints on the issue here would be very helpful.
>>> Thank you in advance.
>>>
>>> Kind regards,
>>> /Katerina
>>>
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

Re: [Gmod-ajax] Problem loading jbrowse page

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

Hi Katerina,

A few things to check:

1. Is apache actually running? Try 'sudo /etc/init.d/apache2 restart' and
see if the last line of the output starts with 'OK' (this seems like it's
probably the problem)

2. Is JBrowse in the right place? From your description, I would guess it's
in /var/www/html/jbrowse but if not, I don't think you're using the right
URL.

3. Make sure the IP address is right.  Check the output of ifconfig.

Scott




On Tue, Mar 10, 2020 at 10:04 AM Katerina Pa <kat...@gm...>
wrote:

> Hello,
>
> I have downloaded and installed jbrowse in /var/www running setup.sh.
> After installing some missing modules, everything was fine and I got the
> messages that volvox is ready to see online. But when I try to open
> http://my.IP.address/jbrowse/index.html?data=sample_data/json/volvox
> <http://157.193.228.78/jbrowse/index.html?data=sample_data/json/volvox>
> or just
> http://my.IP.address/jbrowse/
> I get :
>
> The connection has timed out
>
> The server at xxx.xxx.xxx.xx is taking too long to respond.
>
>     The site could be temporarily unavailable or too busy. Try again in a
> few moments.
>     If you are unable to load any pages, check your computer’s network
> connection.
>     If your computer or network is protected by a firewall or proxy, make
> sure that Firefox is permitted to access the Web.
>
> I am not quite sure what the problem is.  Is it just that the server is
> too slow to respond or could it be sth else? I have installed jbrowse in
> Ubuntu 16.04.6 LTS.
> There should also be apache available, since when I do
> which apache2
> I get
> /usr/sbin/apache2
>
> Any hints on the issue here would be very helpful.
> Thank you in advance.
>
> Kind regards,
> /Katerina
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

[Gmod-ajax] Problem loading jbrowse page

[Katerina Pa <kat...@gm...>]

Hello,

I have downloaded and installed jbrowse in /var/www running setup.sh.
After installing some missing modules, everything was fine and I got the
messages that volvox is ready to see online. But when I try to open
http://my.IP.address/jbrowse/index.html?data=sample_data/json/volvox
<http://157.193.228.78/jbrowse/index.html?data=sample_data/json/volvox>
or just
http://my.IP.address/jbrowse/
I get :

The connection has timed out

The server at xxx.xxx.xxx.xx is taking too long to respond.

    The site could be temporarily unavailable or too busy. Try again in a
few moments.
    If you are unable to load any pages, check your computer’s network
connection.
    If your computer or network is protected by a firewall or proxy, make
sure that Firefox is permitted to access the Web.

I am not quite sure what the problem is.  Is it just that the server is too
slow to respond or could it be sth else? I have installed jbrowse in
Ubuntu 16.04.6 LTS.
There should also be apache available, since when I do
which apache2
I get
/usr/sbin/apache2

Any hints on the issue here would be very helpful.
Thank you in advance.

Kind regards,
/Katerina

Re: [Gmod-ajax] orientation disabling in BED files

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

It seems like something is happening where the strand is set to -1 by a
parsing library that we depend on rather than the jbrowse code doing this

I opened this issue to track this
https://github.com/GMOD/jbrowse/issues/1479 but don't have a quick fix
unfortunately


-Colin

On Sun, Mar 8, 2020 at 10:07 PM Michał T. Lorenc <m.t...@gm...>
wrote:

> Hi all,
> I have a BED file :
> NbV1Ch01        18776453        18777002        MACS2_peak_1486 34      .
>       2.35549 5.48617 3.42439 437
>
> However, JBrowse/Apollo shows that entries show to the left side. Is there
> a way to disable orientation?
>
> Thank you in advance,
>
> Michal
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] orientation disabling in BED files

[Michał T. L. <m.t...@gm...>]

Hi all,
I have a BED file :
NbV1Ch01        18776453        18777002        MACS2_peak_1486 34      .
    2.35549 5.48617 3.42439 437

However, JBrowse/Apollo shows that entries show to the left side. Is there
a way to disable orientation?

Thank you in advance,

Michal