[Gmod-ajax] Using only tracks

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[Gmod-ajax] Using only tracks

Krzyzanowski, Michelle

For now, I am using a iframe, but am trying to use our own tracks.

 

Another colleague set up the tracks according to this website:

 

http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html

 

I have two questions:

 

1.       How do I get it to not include the volvox sample data

2.      Are the bigwig files as made through the link above compatible with JBrowse?

 

Thank you.

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

919-485-5648

 

From: Ben Bimber [mailto:[hidden email]]
Sent: Tuesday, June 06, 2017 12:51 PM
To: Nathan Dunn <[hidden email]>
Cc: Scott Cain <[hidden email]>; [hidden email]; Krzyzanowski, Michelle <[hidden email]>
Subject: Re: [Gmod-ajax] Incorporate JBrowse into CMS

 

Sure.  I'll put together a quick demo on one of our public sites and try to write up some more about how it works.  

 

 

On Tue, Jun 6, 2017 at 9:44 AM, Nathan Dunn <[hidden email]> wrote:

 

There is also this PR written by Colin that attempts to do this with Drupal / Tripal.   

 

 

He was able to work around a lot of the css collision issues, by properly scoping (if that’s the word I want) the CSS.  It has the advantage that they are already using dojo, so there didn’t seem to be as many collisions issues with the JS there.    The Apollo project ends up using iFrames, though to avoid multiple collisions issues.

 

Ben,

 

If you have a demo or source-code for how you did that integration, I think many people would be interested (including myself). 

 

Nathan

 

On Jun 6, 2017, at 8:50 AM, Ben Bimber <[hidden email]> wrote:

 

Hello,

 

It sounds like your goal is integration w/ an established CMS; however, a while ago I wrote a module for LabKey Server (https://www.labkey.org), a fairly widely used platform for managing scientific data.  The module is part of DISCVR-Seq (https://github.com/bbimber/discvr-seq/wiki).  This module essentially wraps JBrowse, such that the user can take genomes and resources managed in LabKey and make custom sessions more or less on the fly (i.e. deal w/ all the backend).  Even if not directly of interest, the way we wrapped the JBrowse app (which actually didnt take very much) might be of interest.  There are not terribly thorough docs on this; however, I can answer questions if anyone is interested.

 

-Ben

 

On Tue, Jun 6, 2017 at 8:15 AM, Scott Cain <[hidden email]> wrote:

Hi Michelle,

 

Directly incorporating JBrowse into other pages can be done in some instances but sorting out conflicts between javascript and css can be quite a hassle.  Many people end up using JBrowse in an iframe, although that doesn't always work in the context of a CMS--it all depends.

 

Scott

 

 

On Tue, Jun 6, 2017 at 11:08 AM, Krzyzanowski, Michelle <[hidden email]> wrote:

I’ll check into that, Scott.

 

I have an entirely different question though.  I need to essentially take index.html and incorporate it into the CMS are website uses.  I have included the basic html and included the css and js, however, nothing shows.  I’m guessing I am going to have to modify some directories. 

 

So the new webpage would be outside of the JBrowse folder.

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 

From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, June 06, 2017 10:27 AM
To: Krzyzanowski, Michelle <[hidden email]>
Cc: Colin <[hidden email]>; [hidden email]
Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

Hi Michelle,

 

I assume you're seeing the same thing I am, which is that every track has a pink box with a 404 not found message.  If you look in the apache error log, you'll find the exact path that JBrowse is looking in for the files that it needs.  Normally, the files in the sample_data directory are where they are "supposed" to be automatically (which is to say, they are there when the JBrowse zip file is unpacked).  The question is, where are those files now?

 

Scott

 

 

On Tue, Jun 6, 2017 at 10:07 AM, Krzyzanowski, Michelle <[hidden email]> wrote:

I apologize.  I am looking at this link:

 

http://54.226.19.179/jbrowse/JBrowse-1.12.3/index.html?data=sample_data%2Fjson%2Fvolvox&loc=ctgA%3A20003..30003&tracks=DNA&highlight=

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 

From: Colin [mailto:[hidden email]]
Sent: Monday, June 05, 2017 10:59 AM
To: Scott Cain <[hidden email]>
Cc: Krzyzanowski, Michelle <[hidden email]>; [hidden email]


Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

Normally running the prepare-refseqs.pl would at least create a "Reference sequence" track on the sidebar, so it is weird that your browser at http://54.226.19.179/jbrowse/JBrowse-1.12.3/ doesn't contain a reference sequence track.

 

Did the setup.sh ever complete without errors? Wondering if maybe the Perl pre-requisites step still didn't finish

 

 

-Colin

 

On Mon, Jun 5, 2017 at 10:33 AM, Scott Cain <[hidden email]> wrote:

Hi Michelle,

 

The prepare-refseqs.pl script only gets the fasta sequence ready to display individual residues in JBrowse.  To get feature tracks, you need to use a source of features, like a GFF file.  If you're following the quick start tutorial, you'll see a command like this:

 

bin/biodb-to-json.pl --conf docs/tutorial/conf_files/volvox.json

 

that configuration file has the information in it for finding the volvox GFF file and what data are in it.

Scott

 

 

On Mon, Jun 5, 2017 at 10:19 AM, Krzyzanowski, Michelle <[hidden email]> wrote:

Here is the url:

 

http://54.226.19.179/jbrowse/JBrowse-1.12.3/index.html?loc=ctgA%3A20003..30003&tracks=&highlight=

 

I was simply using the Volvox test data, so my command was:

 

bin/prepare-refseqs.pl --fasta docs/tutorial/data_files/volvox.fa

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 

From: Colin [mailto:[hidden email]]
Sent: Monday, June 05, 2017 10:04 AM
To: Krzyzanowski, Michelle <[hidden email]>
Cc: Scott Cain <[hidden email]>; [hidden email]


Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

What was your prepare-refseqs command?

 

It is not normally necessary to move refSeqs.json files around or other things like the github issue that you linked there.

 

You can maybe look at http://gmod.org/wiki/JBrowse_FAQ#How_do_I_load_my_genome_as_a_FASTA_file.3F for the "simple overview" of loading the genome

 

-Colin

 

On Mon, Jun 5, 2017 at 8:12 AM, Krzyzanowski, Michelle <[hidden email]> wrote:

Hi Scott,

 

Thank you for that line of code.  It seemed to help.

 

However, I do not see any data.  I attached the screenshot of what JBrowse looks like.  I tried doing this:

 

https://github.com/GMOD/jbrowse/issues/549

 

However, it didn’t fix it.

 

Michelle Krzyzanowski

 

From: Scott Cain [mailto:[hidden email]]
Sent: Friday, June 02, 2017 5:18 PM
To: Krzyzanowski, Michelle <[hidden email]>; [hidden email]


Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

Hi Michelle,

 

Please keep the jbrowse mailing cc'ed so other people can chime in with suggests and the discussion can be archived.

 

The OS matters because different flavors of Linux have different package management systems, of which apt is only one.

 

I suspect it failed because the CPAN system (which installs perl modules) is caching the result from before without checking that there is new stuff that it needs to take into account.  Rather that trying to walk you through cleaning that up, I'd suggest that you install some other packages with apt.  This will install the perl module that the installer is currently tripping one and some others as well.  Do this:

 

  sudo apt-get install libhash-merge-perl libjson-xs-perl libjson-perl liblist-moreutils-perl libperlio-gzip-perl libparse-recdescent-perl liblocal-lib-perl libdb-file-perl libxml-parser-perl libbio-perl-perl

 

(that's all one really long line.)  If it asks you to install other stuff, answer yes.  When that is done running, try the jbrowse setup script again.

 

Scott

 

 

On Fri, Jun 2, 2017 at 3:27 PM, Krzyzanowski, Michelle <[hidden email]> wrote:

Hi Scott,

 

I’m not sure why OS matters since this is on the webserver, not local (unless I’m misunderstanding how to install JBrowse).

 

I conducted the sudo install and it ran, and suggested I also install db5.3-doc, which I also did.  Reran setup.sh and still have the failure.

 

Thank you.

 

Michelle

 

From: Scott Cain [mailto:[hidden email]]
Sent: Friday, June 02, 2017 3:14 PM
To: Krzyzanowski, Michelle <[hidden email]>
Cc: [hidden email]
Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

Hi Michelle,

 

Take a look at this:

 

 

The most immediate problem I think is that you need libexpat (of course, there may be others after you fix this).  You didn't mention what OS you're using--hopefully it's one that uses apt-get.

 

Scott

 

 

On Fri, Jun 2, 2017 at 12:53 PM, Krzyzanowski, Michelle <[hidden email]> wrote:

The Perl prerequisites step is failing, but every other step works.  I have attached the setup.log file.

 

Legacy scripts wig-to-json.pl and bam-to-json.pl have removed from setup. Their functionality has been superseded by add-bam-track.pl and add-bw-track.pl. If you require the old versions, run 'setup.sh legacy'.

Installing javascript dependencies ...Detected precompiled version.

done

Gathering system information ...done

Installing Perl prerequisites ... failed.  See setup.log file for error messages. As a first troubleshooting step, make sure development libraries and header files for GD, Zlib, and libpng are installed and try again.

 

Formatting Volvox example data ... done.

To see the volvox example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/volvox.

 

Formatting Yeast example data ... done.

To see the yeast example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/yeast.

Legacy scripts wig-to-json.pl and bam-to-json.pl have removed from setup. Their functionality has been superseded by add-bam-track.pl and add-bw-track.pl. If you require the old versions, run 'setup.sh legacy'.

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 


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GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



 

--

------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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--

------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research

 



 

--

------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



 

--

------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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Re: Using only tracks

Colin
1. To not include volvox data, simply remove the "sample_data" directory. You might also delete your existing "data" directory since it looks like this had been prepared with prepare-refseqs on the volvox fasta

2. To load other data, just use prepare-refseqs.pl on your own genome, and for bigwig, see http://gmod.org/wiki/JBrowse_FAQ#How_do_I_set_up_a_BigWig_file.3F


-Colin

On Tue, Jun 6, 2017 at 1:28 PM, Krzyzanowski, Michelle <[hidden email]> wrote:

For now, I am using a iframe, but am trying to use our own tracks.

 

Another colleague set up the tracks according to this website:

 

http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html

 

I have two questions:

 

1.       How do I get it to not include the volvox sample data

2.      Are the bigwig files as made through the link above compatible with JBrowse?

 

Thank you.

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" value="+19194855648" target="_blank">919-485-5648

 

From: Ben Bimber [mailto:[hidden email]]
Sent: Tuesday, June 06, 2017 12:51 PM
To: Nathan Dunn <[hidden email]>
Cc: Scott Cain <[hidden email]>; [hidden email]; Krzyzanowski, Michelle <[hidden email]>
Subject: Re: [Gmod-ajax] Incorporate JBrowse into CMS

 

Sure.  I'll put together a quick demo on one of our public sites and try to write up some more about how it works.  

 

 

On Tue, Jun 6, 2017 at 9:44 AM, Nathan Dunn <[hidden email]> wrote:

 

There is also this PR written by Colin that attempts to do this with Drupal / Tripal.   

 

 

He was able to work around a lot of the css collision issues, by properly scoping (if that’s the word I want) the CSS.  It has the advantage that they are already using dojo, so there didn’t seem to be as many collisions issues with the JS there.    The Apollo project ends up using iFrames, though to avoid multiple collisions issues.

 

Ben,

 

If you have a demo or source-code for how you did that integration, I think many people would be interested (including myself). 

 

Nathan

 

On Jun 6, 2017, at 8:50 AM, Ben Bimber <[hidden email]> wrote:

 

Hello,

 

It sounds like your goal is integration w/ an established CMS; however, a while ago I wrote a module for LabKey Server (https://www.labkey.org), a fairly widely used platform for managing scientific data.  The module is part of DISCVR-Seq (https://github.com/bbimber/discvr-seq/wiki).  This module essentially wraps JBrowse, such that the user can take genomes and resources managed in LabKey and make custom sessions more or less on the fly (i.e. deal w/ all the backend).  Even if not directly of interest, the way we wrapped the JBrowse app (which actually didnt take very much) might be of interest.  There are not terribly thorough docs on this; however, I can answer questions if anyone is interested.

 

-Ben

 

On Tue, Jun 6, 2017 at 8:15 AM, Scott Cain <[hidden email]> wrote:

Hi Michelle,

 

Directly incorporating JBrowse into other pages can be done in some instances but sorting out conflicts between javascript and css can be quite a hassle.  Many people end up using JBrowse in an iframe, although that doesn't always work in the context of a CMS--it all depends.

 

Scott

 

 

On Tue, Jun 6, 2017 at 11:08 AM, Krzyzanowski, Michelle <[hidden email]> wrote:

I’ll check into that, Scott.

 

I have an entirely different question though.  I need to essentially take index.html and incorporate it into the CMS are website uses.  I have included the basic html and included the css and js, however, nothing shows.  I’m guessing I am going to have to modify some directories. 

 

So the new webpage would be outside of the JBrowse folder.

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 

From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, June 06, 2017 10:27 AM
To: Krzyzanowski, Michelle <[hidden email]>
Cc: Colin <[hidden email]>; [hidden email]
Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

Hi Michelle,

 

I assume you're seeing the same thing I am, which is that every track has a pink box with a 404 not found message.  If you look in the apache error log, you'll find the exact path that JBrowse is looking in for the files that it needs.  Normally, the files in the sample_data directory are where they are "supposed" to be automatically (which is to say, they are there when the JBrowse zip file is unpacked).  The question is, where are those files now?

 

Scott

 

 

On Tue, Jun 6, 2017 at 10:07 AM, Krzyzanowski, Michelle <[hidden email]> wrote:

I apologize.  I am looking at this link:

 

http://54.226.19.179/jbrowse/JBrowse-1.12.3/index.html?data=sample_data%2Fjson%2Fvolvox&loc=ctgA%3A20003..30003&tracks=DNA&highlight=

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 

From: Colin [mailto:[hidden email]]
Sent: Monday, June 05, 2017 10:59 AM
To: Scott Cain <[hidden email]>
Cc: Krzyzanowski, Michelle <[hidden email]>; [hidden email]


Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

Normally running the prepare-refseqs.pl would at least create a "Reference sequence" track on the sidebar, so it is weird that your browser at http://54.226.19.179/jbrowse/JBrowse-1.12.3/ doesn't contain a reference sequence track.

 

Did the setup.sh ever complete without errors? Wondering if maybe the Perl pre-requisites step still didn't finish

 

 

-Colin

 

On Mon, Jun 5, 2017 at 10:33 AM, Scott Cain <[hidden email]> wrote:

Hi Michelle,

 

The prepare-refseqs.pl script only gets the fasta sequence ready to display individual residues in JBrowse.  To get feature tracks, you need to use a source of features, like a GFF file.  If you're following the quick start tutorial, you'll see a command like this:

 

bin/biodb-to-json.pl --conf docs/tutorial/conf_files/volvox.json

 

that configuration file has the information in it for finding the volvox GFF file and what data are in it.

Scott

 

 

On Mon, Jun 5, 2017 at 10:19 AM, Krzyzanowski, Michelle <[hidden email]> wrote:

Here is the url:

 

http://54.226.19.179/jbrowse/JBrowse-1.12.3/index.html?loc=ctgA%3A20003..30003&tracks=&highlight=

 

I was simply using the Volvox test data, so my command was:

 

bin/prepare-refseqs.pl --fasta docs/tutorial/data_files/volvox.fa

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 

From: Colin [mailto:[hidden email]]
Sent: Monday, June 05, 2017 10:04 AM
To: Krzyzanowski, Michelle <[hidden email]>
Cc: Scott Cain <[hidden email]>; [hidden email]


Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

What was your prepare-refseqs command?

 

It is not normally necessary to move refSeqs.json files around or other things like the github issue that you linked there.

 

You can maybe look at http://gmod.org/wiki/JBrowse_FAQ#How_do_I_load_my_genome_as_a_FASTA_file.3F for the "simple overview" of loading the genome

 

-Colin

 

On Mon, Jun 5, 2017 at 8:12 AM, Krzyzanowski, Michelle <[hidden email]> wrote:

Hi Scott,

 

Thank you for that line of code.  It seemed to help.

 

However, I do not see any data.  I attached the screenshot of what JBrowse looks like.  I tried doing this:

 

https://github.com/GMOD/jbrowse/issues/549

 

However, it didn’t fix it.

 

Michelle Krzyzanowski

 

From: Scott Cain [mailto:[hidden email]]
Sent: Friday, June 02, 2017 5:18 PM
To: Krzyzanowski, Michelle <[hidden email]>; [hidden email]


Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

Hi Michelle,

 

Please keep the jbrowse mailing cc'ed so other people can chime in with suggests and the discussion can be archived.

 

The OS matters because different flavors of Linux have different package management systems, of which apt is only one.

 

I suspect it failed because the CPAN system (which installs perl modules) is caching the result from before without checking that there is new stuff that it needs to take into account.  Rather that trying to walk you through cleaning that up, I'd suggest that you install some other packages with apt.  This will install the perl module that the installer is currently tripping one and some others as well.  Do this:

 

  sudo apt-get install libhash-merge-perl libjson-xs-perl libjson-perl liblist-moreutils-perl libperlio-gzip-perl libparse-recdescent-perl liblocal-lib-perl libdb-file-perl libxml-parser-perl libbio-perl-perl

 

(that's all one really long line.)  If it asks you to install other stuff, answer yes.  When that is done running, try the jbrowse setup script again.

 

Scott

 

 

On Fri, Jun 2, 2017 at 3:27 PM, Krzyzanowski, Michelle <[hidden email]> wrote:

Hi Scott,

 

I’m not sure why OS matters since this is on the webserver, not local (unless I’m misunderstanding how to install JBrowse).

 

I conducted the sudo install and it ran, and suggested I also install db5.3-doc, which I also did.  Reran setup.sh and still have the failure.

 

Thank you.

 

Michelle

 

From: Scott Cain [mailto:[hidden email]]
Sent: Friday, June 02, 2017 3:14 PM
To: Krzyzanowski, Michelle <[hidden email]>
Cc: [hidden email]
Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

Hi Michelle,

 

Take a look at this:

 

 

The most immediate problem I think is that you need libexpat (of course, there may be others after you fix this).  You didn't mention what OS you're using--hopefully it's one that uses apt-get.

 

Scott

 

 

On Fri, Jun 2, 2017 at 12:53 PM, Krzyzanowski, Michelle <[hidden email]> wrote:

The Perl prerequisites step is failing, but every other step works.  I have attached the setup.log file.

 

Legacy scripts wig-to-json.pl and bam-to-json.pl have removed from setup. Their functionality has been superseded by add-bam-track.pl and add-bw-track.pl. If you require the old versions, run 'setup.sh legacy'.

Installing javascript dependencies ...Detected precompiled version.

done

Gathering system information ...done

Installing Perl prerequisites ... failed.  See setup.log file for error messages. As a first troubleshooting step, make sure development libraries and header files for GD, Zlib, and libpng are installed and try again.

 

Formatting Volvox example data ... done.

To see the volvox example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/volvox.

 

Formatting Yeast example data ... done.

To see the yeast example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/yeast.

Legacy scripts wig-to-json.pl and bam-to-json.pl have removed from setup. Their functionality has been superseded by add-bam-track.pl and add-bw-track.pl. If you require the old versions, run 'setup.sh legacy'.

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 


------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax



 

--

------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



 

--

------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

 



 

--

------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research

 



 

--

------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



 

--

------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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Re: Using only tracks

Scott Cain
In reply to this post by Krzyzanowski, Michelle
Hi Michelle,

Would it be possible to take a step back and give us an overview of what you are trying to do?  I feel a little like the blind men and the elephant (https://en.wikipedia.org/wiki/Blind_men_and_an_elephant) as we try to help you solve particular pieces, whereas it might be a better use of everyone's time if we knew what you're trying to do.  Items that might help:

* what is the nature of the CMS you're working with?  Something built in house or from the outside world (like Drupal)?  What is the javascript infrastructure like (JQuery or the like, for example)?

* Do you need to support more than one organism?

* Have you been mandated to use JBrowse or are you just kicking the tires? (I ask this because of your reference to track hubs, which is a UCSC genome browser thing, not a JBrowse thing.)

* Are there any other "specialty" items that you will need JBrowse to do?  (I realize this is vague and so you may not know the answer.)

Thanks,
Scott


On Tue, Jun 6, 2017 at 1:28 PM, Krzyzanowski, Michelle <[hidden email]> wrote:

For now, I am using a iframe, but am trying to use our own tracks.

 

Another colleague set up the tracks according to this website:

 

http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html

 

I have two questions:

 

1.       How do I get it to not include the volvox sample data

2.      Are the bigwig files as made through the link above compatible with JBrowse?

 

Thank you.

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" value="+19194855648" target="_blank">919-485-5648

 

From: Ben Bimber [mailto:[hidden email]]
Sent: Tuesday, June 06, 2017 12:51 PM
To: Nathan Dunn <[hidden email]>
Cc: Scott Cain <[hidden email]>; [hidden email]; Krzyzanowski, Michelle <[hidden email]>
Subject: Re: [Gmod-ajax] Incorporate JBrowse into CMS

 

Sure.  I'll put together a quick demo on one of our public sites and try to write up some more about how it works.  

 

 

On Tue, Jun 6, 2017 at 9:44 AM, Nathan Dunn <[hidden email]> wrote:

 

There is also this PR written by Colin that attempts to do this with Drupal / Tripal.   

 

 

He was able to work around a lot of the css collision issues, by properly scoping (if that’s the word I want) the CSS.  It has the advantage that they are already using dojo, so there didn’t seem to be as many collisions issues with the JS there.    The Apollo project ends up using iFrames, though to avoid multiple collisions issues.

 

Ben,

 

If you have a demo or source-code for how you did that integration, I think many people would be interested (including myself). 

 

Nathan

 

On Jun 6, 2017, at 8:50 AM, Ben Bimber <[hidden email]> wrote:

 

Hello,

 

It sounds like your goal is integration w/ an established CMS; however, a while ago I wrote a module for LabKey Server (https://www.labkey.org), a fairly widely used platform for managing scientific data.  The module is part of DISCVR-Seq (https://github.com/bbimber/discvr-seq/wiki).  This module essentially wraps JBrowse, such that the user can take genomes and resources managed in LabKey and make custom sessions more or less on the fly (i.e. deal w/ all the backend).  Even if not directly of interest, the way we wrapped the JBrowse app (which actually didnt take very much) might be of interest.  There are not terribly thorough docs on this; however, I can answer questions if anyone is interested.

 

-Ben

 

On Tue, Jun 6, 2017 at 8:15 AM, Scott Cain <[hidden email]> wrote:

Hi Michelle,

 

Directly incorporating JBrowse into other pages can be done in some instances but sorting out conflicts between javascript and css can be quite a hassle.  Many people end up using JBrowse in an iframe, although that doesn't always work in the context of a CMS--it all depends.

 

Scott

 

 

On Tue, Jun 6, 2017 at 11:08 AM, Krzyzanowski, Michelle <[hidden email]> wrote:

I’ll check into that, Scott.

 

I have an entirely different question though.  I need to essentially take index.html and incorporate it into the CMS are website uses.  I have included the basic html and included the css and js, however, nothing shows.  I’m guessing I am going to have to modify some directories. 

 

So the new webpage would be outside of the JBrowse folder.

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 

From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, June 06, 2017 10:27 AM
To: Krzyzanowski, Michelle <[hidden email]>
Cc: Colin <[hidden email]>; [hidden email]
Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

Hi Michelle,

 

I assume you're seeing the same thing I am, which is that every track has a pink box with a 404 not found message.  If you look in the apache error log, you'll find the exact path that JBrowse is looking in for the files that it needs.  Normally, the files in the sample_data directory are where they are "supposed" to be automatically (which is to say, they are there when the JBrowse zip file is unpacked).  The question is, where are those files now?

 

Scott

 

 

On Tue, Jun 6, 2017 at 10:07 AM, Krzyzanowski, Michelle <[hidden email]> wrote:

I apologize.  I am looking at this link:

 

http://54.226.19.179/jbrowse/JBrowse-1.12.3/index.html?data=sample_data%2Fjson%2Fvolvox&loc=ctgA%3A20003..30003&tracks=DNA&highlight=

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 

From: Colin [mailto:[hidden email]]
Sent: Monday, June 05, 2017 10:59 AM
To: Scott Cain <[hidden email]>
Cc: Krzyzanowski, Michelle <[hidden email]>; [hidden email]


Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

Normally running the prepare-refseqs.pl would at least create a "Reference sequence" track on the sidebar, so it is weird that your browser at http://54.226.19.179/jbrowse/JBrowse-1.12.3/ doesn't contain a reference sequence track.

 

Did the setup.sh ever complete without errors? Wondering if maybe the Perl pre-requisites step still didn't finish

 

 

-Colin

 

On Mon, Jun 5, 2017 at 10:33 AM, Scott Cain <[hidden email]> wrote:

Hi Michelle,

 

The prepare-refseqs.pl script only gets the fasta sequence ready to display individual residues in JBrowse.  To get feature tracks, you need to use a source of features, like a GFF file.  If you're following the quick start tutorial, you'll see a command like this:

 

bin/biodb-to-json.pl --conf docs/tutorial/conf_files/volvox.json

 

that configuration file has the information in it for finding the volvox GFF file and what data are in it.

Scott

 

 

On Mon, Jun 5, 2017 at 10:19 AM, Krzyzanowski, Michelle <[hidden email]> wrote:

Here is the url:

 

http://54.226.19.179/jbrowse/JBrowse-1.12.3/index.html?loc=ctgA%3A20003..30003&tracks=&highlight=

 

I was simply using the Volvox test data, so my command was:

 

bin/prepare-refseqs.pl --fasta docs/tutorial/data_files/volvox.fa

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 

From: Colin [mailto:[hidden email]]
Sent: Monday, June 05, 2017 10:04 AM
To: Krzyzanowski, Michelle <[hidden email]>
Cc: Scott Cain <[hidden email]>; [hidden email]


Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

What was your prepare-refseqs command?

 

It is not normally necessary to move refSeqs.json files around or other things like the github issue that you linked there.

 

You can maybe look at http://gmod.org/wiki/JBrowse_FAQ#How_do_I_load_my_genome_as_a_FASTA_file.3F for the "simple overview" of loading the genome

 

-Colin

 

On Mon, Jun 5, 2017 at 8:12 AM, Krzyzanowski, Michelle <[hidden email]> wrote:

Hi Scott,

 

Thank you for that line of code.  It seemed to help.

 

However, I do not see any data.  I attached the screenshot of what JBrowse looks like.  I tried doing this:

 

https://github.com/GMOD/jbrowse/issues/549

 

However, it didn’t fix it.

 

Michelle Krzyzanowski

 

From: Scott Cain [mailto:[hidden email]]
Sent: Friday, June 02, 2017 5:18 PM
To: Krzyzanowski, Michelle <[hidden email]>; [hidden email]


Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

Hi Michelle,

 

Please keep the jbrowse mailing cc'ed so other people can chime in with suggests and the discussion can be archived.

 

The OS matters because different flavors of Linux have different package management systems, of which apt is only one.

 

I suspect it failed because the CPAN system (which installs perl modules) is caching the result from before without checking that there is new stuff that it needs to take into account.  Rather that trying to walk you through cleaning that up, I'd suggest that you install some other packages with apt.  This will install the perl module that the installer is currently tripping one and some others as well.  Do this:

 

  sudo apt-get install libhash-merge-perl libjson-xs-perl libjson-perl liblist-moreutils-perl libperlio-gzip-perl libparse-recdescent-perl liblocal-lib-perl libdb-file-perl libxml-parser-perl libbio-perl-perl

 

(that's all one really long line.)  If it asks you to install other stuff, answer yes.  When that is done running, try the jbrowse setup script again.

 

Scott

 

 

On Fri, Jun 2, 2017 at 3:27 PM, Krzyzanowski, Michelle <[hidden email]> wrote:

Hi Scott,

 

I’m not sure why OS matters since this is on the webserver, not local (unless I’m misunderstanding how to install JBrowse).

 

I conducted the sudo install and it ran, and suggested I also install db5.3-doc, which I also did.  Reran setup.sh and still have the failure.

 

Thank you.

 

Michelle

 

From: Scott Cain [mailto:[hidden email]]
Sent: Friday, June 02, 2017 3:14 PM
To: Krzyzanowski, Michelle <[hidden email]>
Cc: [hidden email]
Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

Hi Michelle,

 

Take a look at this:

 

 

The most immediate problem I think is that you need libexpat (of course, there may be others after you fix this).  You didn't mention what OS you're using--hopefully it's one that uses apt-get.

 

Scott

 

 

On Fri, Jun 2, 2017 at 12:53 PM, Krzyzanowski, Michelle <[hidden email]> wrote:

The Perl prerequisites step is failing, but every other step works.  I have attached the setup.log file.

 

Legacy scripts wig-to-json.pl and bam-to-json.pl have removed from setup. Their functionality has been superseded by add-bam-track.pl and add-bw-track.pl. If you require the old versions, run 'setup.sh legacy'.

Installing javascript dependencies ...Detected precompiled version.

done

Gathering system information ...done

Installing Perl prerequisites ... failed.  See setup.log file for error messages. As a first troubleshooting step, make sure development libraries and header files for GD, Zlib, and libpng are installed and try again.

 

Formatting Volvox example data ... done.

To see the volvox example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/volvox.

 

Formatting Yeast example data ... done.

To see the yeast example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/yeast.

Legacy scripts wig-to-json.pl and bam-to-json.pl have removed from setup. Their functionality has been superseded by add-bam-track.pl and add-bw-track.pl. If you require the old versions, run 'setup.sh legacy'.

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 


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--

------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



 

--

------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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--

------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research

 



 

--

------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



 

--

------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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Ontario Institute for Cancer Research

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Re: Using only tracks

Krzyzanowski, Michelle

Hi Scott,

 

The website uses SilverStripe for the CMS.

 

We will likely need to support both human and mouse in the future.

 

I am kicking the tires.  No one else here has experience integrating a genome browser.  The PM had told another colleague to create the tracks, thinking it could be used by JBrowse.

 

I am not sure about any other specialty items.

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

919-485-5648

 

From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, June 06, 2017 2:20 PM
To: Krzyzanowski, Michelle <[hidden email]>
Cc: [hidden email]
Subject: Re: [Gmod-ajax] Using only tracks

 

Hi Michelle,

 

Would it be possible to take a step back and give us an overview of what you are trying to do?  I feel a little like the blind men and the elephant (https://en.wikipedia.org/wiki/Blind_men_and_an_elephant) as we try to help you solve particular pieces, whereas it might be a better use of everyone's time if we knew what you're trying to do.  Items that might help:

 

* what is the nature of the CMS you're working with?  Something built in house or from the outside world (like Drupal)?  What is the javascript infrastructure like (JQuery or the like, for example)?

 

* Do you need to support more than one organism?

 

* Have you been mandated to use JBrowse or are you just kicking the tires? (I ask this because of your reference to track hubs, which is a UCSC genome browser thing, not a JBrowse thing.)

 

* Are there any other "specialty" items that you will need JBrowse to do?  (I realize this is vague and so you may not know the answer.)

 

Thanks,

Scott

 

 

On Tue, Jun 6, 2017 at 1:28 PM, Krzyzanowski, Michelle <[hidden email]> wrote:

For now, I am using a iframe, but am trying to use our own tracks.

 

Another colleague set up the tracks according to this website:

 

http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html

 

I have two questions:

 

1.       How do I get it to not include the volvox sample data

2.      Are the bigwig files as made through the link above compatible with JBrowse?

 

Thank you.

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 

From: Ben Bimber [mailto:[hidden email]]
Sent: Tuesday, June 06, 2017 12:51 PM
To: Nathan Dunn <[hidden email]>
Cc: Scott Cain <[hidden email]>; [hidden email]; Krzyzanowski, Michelle <[hidden email]>
Subject: Re: [Gmod-ajax] Incorporate JBrowse into CMS

 

Sure.  I'll put together a quick demo on one of our public sites and try to write up some more about how it works.  

 

 

On Tue, Jun 6, 2017 at 9:44 AM, Nathan Dunn <[hidden email]> wrote:

 

There is also this PR written by Colin that attempts to do this with Drupal / Tripal.   

 

 

He was able to work around a lot of the css collision issues, by properly scoping (if that’s the word I want) the CSS.  It has the advantage that they are already using dojo, so there didn’t seem to be as many collisions issues with the JS there.    The Apollo project ends up using iFrames, though to avoid multiple collisions issues.

 

Ben,

 

If you have a demo or source-code for how you did that integration, I think many people would be interested (including myself). 

 

Nathan

 

On Jun 6, 2017, at 8:50 AM, Ben Bimber <[hidden email]> wrote:

 

Hello,

 

It sounds like your goal is integration w/ an established CMS; however, a while ago I wrote a module for LabKey Server (https://www.labkey.org), a fairly widely used platform for managing scientific data.  The module is part of DISCVR-Seq (https://github.com/bbimber/discvr-seq/wiki).  This module essentially wraps JBrowse, such that the user can take genomes and resources managed in LabKey and make custom sessions more or less on the fly (i.e. deal w/ all the backend).  Even if not directly of interest, the way we wrapped the JBrowse app (which actually didnt take very much) might be of interest.  There are not terribly thorough docs on this; however, I can answer questions if anyone is interested.

 

-Ben

 

On Tue, Jun 6, 2017 at 8:15 AM, Scott Cain <[hidden email]> wrote:

Hi Michelle,

 

Directly incorporating JBrowse into other pages can be done in some instances but sorting out conflicts between javascript and css can be quite a hassle.  Many people end up using JBrowse in an iframe, although that doesn't always work in the context of a CMS--it all depends.

 

Scott

 

 

On Tue, Jun 6, 2017 at 11:08 AM, Krzyzanowski, Michelle <[hidden email]> wrote:

I’ll check into that, Scott.

 

I have an entirely different question though.  I need to essentially take index.html and incorporate it into the CMS are website uses.  I have included the basic html and included the css and js, however, nothing shows.  I’m guessing I am going to have to modify some directories. 

 

So the new webpage would be outside of the JBrowse folder.

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 

From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, June 06, 2017 10:27 AM
To: Krzyzanowski, Michelle <[hidden email]>
Cc: Colin <[hidden email]>; [hidden email]
Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

Hi Michelle,

 

I assume you're seeing the same thing I am, which is that every track has a pink box with a 404 not found message.  If you look in the apache error log, you'll find the exact path that JBrowse is looking in for the files that it needs.  Normally, the files in the sample_data directory are where they are "supposed" to be automatically (which is to say, they are there when the JBrowse zip file is unpacked).  The question is, where are those files now?

 

Scott

 

 

On Tue, Jun 6, 2017 at 10:07 AM, Krzyzanowski, Michelle <[hidden email]> wrote:

I apologize.  I am looking at this link:

 

http://54.226.19.179/jbrowse/JBrowse-1.12.3/index.html?data=sample_data%2Fjson%2Fvolvox&loc=ctgA%3A20003..30003&tracks=DNA&highlight=

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 

From: Colin [mailto:[hidden email]]
Sent: Monday, June 05, 2017 10:59 AM
To: Scott Cain <[hidden email]>
Cc: Krzyzanowski, Michelle <[hidden email]>; [hidden email]


Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

Normally running the prepare-refseqs.pl would at least create a "Reference sequence" track on the sidebar, so it is weird that your browser at http://54.226.19.179/jbrowse/JBrowse-1.12.3/ doesn't contain a reference sequence track.

 

Did the setup.sh ever complete without errors? Wondering if maybe the Perl pre-requisites step still didn't finish

 

 

-Colin

 

On Mon, Jun 5, 2017 at 10:33 AM, Scott Cain <[hidden email]> wrote:

Hi Michelle,

 

The prepare-refseqs.pl script only gets the fasta sequence ready to display individual residues in JBrowse.  To get feature tracks, you need to use a source of features, like a GFF file.  If you're following the quick start tutorial, you'll see a command like this:

 

bin/biodb-to-json.pl --conf docs/tutorial/conf_files/volvox.json

 

that configuration file has the information in it for finding the volvox GFF file and what data are in it.

Scott

 

 

On Mon, Jun 5, 2017 at 10:19 AM, Krzyzanowski, Michelle <[hidden email]> wrote:

Here is the url:

 

http://54.226.19.179/jbrowse/JBrowse-1.12.3/index.html?loc=ctgA%3A20003..30003&tracks=&highlight=

 

I was simply using the Volvox test data, so my command was:

 

bin/prepare-refseqs.pl --fasta docs/tutorial/data_files/volvox.fa

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 

From: Colin [mailto:[hidden email]]
Sent: Monday, June 05, 2017 10:04 AM
To: Krzyzanowski, Michelle <[hidden email]>
Cc: Scott Cain <[hidden email]>; [hidden email]


Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

What was your prepare-refseqs command?

 

It is not normally necessary to move refSeqs.json files around or other things like the github issue that you linked there.

 

You can maybe look at http://gmod.org/wiki/JBrowse_FAQ#How_do_I_load_my_genome_as_a_FASTA_file.3F for the "simple overview" of loading the genome

 

-Colin

 

On Mon, Jun 5, 2017 at 8:12 AM, Krzyzanowski, Michelle <[hidden email]> wrote:

Hi Scott,

 

Thank you for that line of code.  It seemed to help.

 

However, I do not see any data.  I attached the screenshot of what JBrowse looks like.  I tried doing this:

 

https://github.com/GMOD/jbrowse/issues/549

 

However, it didn’t fix it.

 

Michelle Krzyzanowski

 

From: Scott Cain [mailto:[hidden email]]
Sent: Friday, June 02, 2017 5:18 PM
To: Krzyzanowski, Michelle <[hidden email]>; [hidden email]


Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

Hi Michelle,

 

Please keep the jbrowse mailing cc'ed so other people can chime in with suggests and the discussion can be archived.

 

The OS matters because different flavors of Linux have different package management systems, of which apt is only one.

 

I suspect it failed because the CPAN system (which installs perl modules) is caching the result from before without checking that there is new stuff that it needs to take into account.  Rather that trying to walk you through cleaning that up, I'd suggest that you install some other packages with apt.  This will install the perl module that the installer is currently tripping one and some others as well.  Do this:

 

  sudo apt-get install libhash-merge-perl libjson-xs-perl libjson-perl liblist-moreutils-perl libperlio-gzip-perl libparse-recdescent-perl liblocal-lib-perl libdb-file-perl libxml-parser-perl libbio-perl-perl

 

(that's all one really long line.)  If it asks you to install other stuff, answer yes.  When that is done running, try the jbrowse setup script again.

 

Scott

 

 

On Fri, Jun 2, 2017 at 3:27 PM, Krzyzanowski, Michelle <[hidden email]> wrote:

Hi Scott,

 

I’m not sure why OS matters since this is on the webserver, not local (unless I’m misunderstanding how to install JBrowse).

 

I conducted the sudo install and it ran, and suggested I also install db5.3-doc, which I also did.  Reran setup.sh and still have the failure.

 

Thank you.

 

Michelle

 

From: Scott Cain [mailto:[hidden email]]
Sent: Friday, June 02, 2017 3:14 PM
To: Krzyzanowski, Michelle <[hidden email]>
Cc: [hidden email]
Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

Hi Michelle,

 

Take a look at this:

 

 

The most immediate problem I think is that you need libexpat (of course, there may be others after you fix this).  You didn't mention what OS you're using--hopefully it's one that uses apt-get.

 

Scott

 

 

On Fri, Jun 2, 2017 at 12:53 PM, Krzyzanowski, Michelle <[hidden email]> wrote:

The Perl prerequisites step is failing, but every other step works.  I have attached the setup.log file.

 

Legacy scripts wig-to-json.pl and bam-to-json.pl have removed from setup. Their functionality has been superseded by add-bam-track.pl and add-bw-track.pl. If you require the old versions, run 'setup.sh legacy'.

Installing javascript dependencies ...Detected precompiled version.

done

Gathering system information ...done

Installing Perl prerequisites ... failed.  See setup.log file for error messages. As a first troubleshooting step, make sure development libraries and header files for GD, Zlib, and libpng are installed and try again.

 

Formatting Volvox example data ... done.

To see the volvox example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/volvox.

 

Formatting Yeast example data ... done.

To see the yeast example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/yeast.

Legacy scripts wig-to-json.pl and bam-to-json.pl have removed from setup. Their functionality has been superseded by add-bam-track.pl and add-bw-track.pl. If you require the old versions, run 'setup.sh legacy'.

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 


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Re: Using only tracks

Scott Cain
Thanks Michelle,

For supporting multiple organisms, you might want to be aware of this going forward:


Basically, you'll want a separate directory for each organism, with their own trackList.json files.  Thinking about that before you start putting in a bunch of data that you'll then want to reorganize is a good idea :-)


Scott


On Tue, Jun 6, 2017 at 2:23 PM, Krzyzanowski, Michelle <[hidden email]> wrote:

Hi Scott,

 

The website uses SilverStripe for the CMS.

 

We will likely need to support both human and mouse in the future.

 

I am kicking the tires.  No one else here has experience integrating a genome browser.  The PM had told another colleague to create the tracks, thinking it could be used by JBrowse.

 

I am not sure about any other specialty items.

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" value="+19194855648" target="_blank">919-485-5648

 

From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, June 06, 2017 2:20 PM
To: Krzyzanowski, Michelle <[hidden email]>
Cc: [hidden email]
Subject: Re: [Gmod-ajax] Using only tracks

 

Hi Michelle,

 

Would it be possible to take a step back and give us an overview of what you are trying to do?  I feel a little like the blind men and the elephant (https://en.wikipedia.org/wiki/Blind_men_and_an_elephant) as we try to help you solve particular pieces, whereas it might be a better use of everyone's time if we knew what you're trying to do.  Items that might help:

 

* what is the nature of the CMS you're working with?  Something built in house or from the outside world (like Drupal)?  What is the javascript infrastructure like (JQuery or the like, for example)?

 

* Do you need to support more than one organism?

 

* Have you been mandated to use JBrowse or are you just kicking the tires? (I ask this because of your reference to track hubs, which is a UCSC genome browser thing, not a JBrowse thing.)

 

* Are there any other "specialty" items that you will need JBrowse to do?  (I realize this is vague and so you may not know the answer.)

 

Thanks,

Scott

 

 

On Tue, Jun 6, 2017 at 1:28 PM, Krzyzanowski, Michelle <[hidden email]> wrote:

For now, I am using a iframe, but am trying to use our own tracks.

 

Another colleague set up the tracks according to this website:

 

http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html

 

I have two questions:

 

1.       How do I get it to not include the volvox sample data

2.      Are the bigwig files as made through the link above compatible with JBrowse?

 

Thank you.

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 

From: Ben Bimber [mailto:[hidden email]]
Sent: Tuesday, June 06, 2017 12:51 PM
To: Nathan Dunn <[hidden email]>
Cc: Scott Cain <[hidden email]>; [hidden email]; Krzyzanowski, Michelle <[hidden email]>
Subject: Re: [Gmod-ajax] Incorporate JBrowse into CMS

 

Sure.  I'll put together a quick demo on one of our public sites and try to write up some more about how it works.  

 

 

On Tue, Jun 6, 2017 at 9:44 AM, Nathan Dunn <[hidden email]> wrote:

 

There is also this PR written by Colin that attempts to do this with Drupal / Tripal.   

 

 

He was able to work around a lot of the css collision issues, by properly scoping (if that’s the word I want) the CSS.  It has the advantage that they are already using dojo, so there didn’t seem to be as many collisions issues with the JS there.    The Apollo project ends up using iFrames, though to avoid multiple collisions issues.

 

Ben,

 

If you have a demo or source-code for how you did that integration, I think many people would be interested (including myself). 

 

Nathan

 

On Jun 6, 2017, at 8:50 AM, Ben Bimber <[hidden email]> wrote:

 

Hello,

 

It sounds like your goal is integration w/ an established CMS; however, a while ago I wrote a module for LabKey Server (https://www.labkey.org), a fairly widely used platform for managing scientific data.  The module is part of DISCVR-Seq (https://github.com/bbimber/discvr-seq/wiki).  This module essentially wraps JBrowse, such that the user can take genomes and resources managed in LabKey and make custom sessions more or less on the fly (i.e. deal w/ all the backend).  Even if not directly of interest, the way we wrapped the JBrowse app (which actually didnt take very much) might be of interest.  There are not terribly thorough docs on this; however, I can answer questions if anyone is interested.

 

-Ben

 

On Tue, Jun 6, 2017 at 8:15 AM, Scott Cain <[hidden email]> wrote:

Hi Michelle,

 

Directly incorporating JBrowse into other pages can be done in some instances but sorting out conflicts between javascript and css can be quite a hassle.  Many people end up using JBrowse in an iframe, although that doesn't always work in the context of a CMS--it all depends.

 

Scott

 

 

On Tue, Jun 6, 2017 at 11:08 AM, Krzyzanowski, Michelle <[hidden email]> wrote:

I’ll check into that, Scott.

 

I have an entirely different question though.  I need to essentially take index.html and incorporate it into the CMS are website uses.  I have included the basic html and included the css and js, however, nothing shows.  I’m guessing I am going to have to modify some directories. 

 

So the new webpage would be outside of the JBrowse folder.

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 

From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, June 06, 2017 10:27 AM
To: Krzyzanowski, Michelle <[hidden email]>
Cc: Colin <[hidden email]>; [hidden email]
Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

Hi Michelle,

 

I assume you're seeing the same thing I am, which is that every track has a pink box with a 404 not found message.  If you look in the apache error log, you'll find the exact path that JBrowse is looking in for the files that it needs.  Normally, the files in the sample_data directory are where they are "supposed" to be automatically (which is to say, they are there when the JBrowse zip file is unpacked).  The question is, where are those files now?

 

Scott

 

 

On Tue, Jun 6, 2017 at 10:07 AM, Krzyzanowski, Michelle <[hidden email]> wrote:

I apologize.  I am looking at this link:

 

http://54.226.19.179/jbrowse/JBrowse-1.12.3/index.html?data=sample_data%2Fjson%2Fvolvox&loc=ctgA%3A20003..30003&tracks=DNA&highlight=

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 

From: Colin [mailto:[hidden email]]
Sent: Monday, June 05, 2017 10:59 AM
To: Scott Cain <[hidden email]>
Cc: Krzyzanowski, Michelle <[hidden email]>; [hidden email]


Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

Normally running the prepare-refseqs.pl would at least create a "Reference sequence" track on the sidebar, so it is weird that your browser at http://54.226.19.179/jbrowse/JBrowse-1.12.3/ doesn't contain a reference sequence track.

 

Did the setup.sh ever complete without errors? Wondering if maybe the Perl pre-requisites step still didn't finish

 

 

-Colin

 

On Mon, Jun 5, 2017 at 10:33 AM, Scott Cain <[hidden email]> wrote:

Hi Michelle,

 

The prepare-refseqs.pl script only gets the fasta sequence ready to display individual residues in JBrowse.  To get feature tracks, you need to use a source of features, like a GFF file.  If you're following the quick start tutorial, you'll see a command like this:

 

bin/biodb-to-json.pl --conf docs/tutorial/conf_files/volvox.json

 

that configuration file has the information in it for finding the volvox GFF file and what data are in it.

Scott

 

 

On Mon, Jun 5, 2017 at 10:19 AM, Krzyzanowski, Michelle <[hidden email]> wrote:

Here is the url:

 

http://54.226.19.179/jbrowse/JBrowse-1.12.3/index.html?loc=ctgA%3A20003..30003&tracks=&highlight=

 

I was simply using the Volvox test data, so my command was:

 

bin/prepare-refseqs.pl --fasta docs/tutorial/data_files/volvox.fa

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 

From: Colin [mailto:[hidden email]]
Sent: Monday, June 05, 2017 10:04 AM
To: Krzyzanowski, Michelle <[hidden email]>
Cc: Scott Cain <[hidden email]>; [hidden email]


Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

What was your prepare-refseqs command?

 

It is not normally necessary to move refSeqs.json files around or other things like the github issue that you linked there.

 

You can maybe look at http://gmod.org/wiki/JBrowse_FAQ#How_do_I_load_my_genome_as_a_FASTA_file.3F for the "simple overview" of loading the genome

 

-Colin

 

On Mon, Jun 5, 2017 at 8:12 AM, Krzyzanowski, Michelle <[hidden email]> wrote:

Hi Scott,

 

Thank you for that line of code.  It seemed to help.

 

However, I do not see any data.  I attached the screenshot of what JBrowse looks like.  I tried doing this:

 

https://github.com/GMOD/jbrowse/issues/549

 

However, it didn’t fix it.

 

Michelle Krzyzanowski

 

From: Scott Cain [mailto:[hidden email]]
Sent: Friday, June 02, 2017 5:18 PM
To: Krzyzanowski, Michelle <[hidden email]>; [hidden email]


Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

Hi Michelle,

 

Please keep the jbrowse mailing cc'ed so other people can chime in with suggests and the discussion can be archived.

 

The OS matters because different flavors of Linux have different package management systems, of which apt is only one.

 

I suspect it failed because the CPAN system (which installs perl modules) is caching the result from before without checking that there is new stuff that it needs to take into account.  Rather that trying to walk you through cleaning that up, I'd suggest that you install some other packages with apt.  This will install the perl module that the installer is currently tripping one and some others as well.  Do this:

 

  sudo apt-get install libhash-merge-perl libjson-xs-perl libjson-perl liblist-moreutils-perl libperlio-gzip-perl libparse-recdescent-perl liblocal-lib-perl libdb-file-perl libxml-parser-perl libbio-perl-perl

 

(that's all one really long line.)  If it asks you to install other stuff, answer yes.  When that is done running, try the jbrowse setup script again.

 

Scott

 

 

On Fri, Jun 2, 2017 at 3:27 PM, Krzyzanowski, Michelle <[hidden email]> wrote:

Hi Scott,

 

I’m not sure why OS matters since this is on the webserver, not local (unless I’m misunderstanding how to install JBrowse).

 

I conducted the sudo install and it ran, and suggested I also install db5.3-doc, which I also did.  Reran setup.sh and still have the failure.

 

Thank you.

 

Michelle

 

From: Scott Cain [mailto:[hidden email]]
Sent: Friday, June 02, 2017 3:14 PM
To: Krzyzanowski, Michelle <[hidden email]>
Cc: [hidden email]
Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

Hi Michelle,

 

Take a look at this:

 

 

The most immediate problem I think is that you need libexpat (of course, there may be others after you fix this).  You didn't mention what OS you're using--hopefully it's one that uses apt-get.

 

Scott

 

 

On Fri, Jun 2, 2017 at 12:53 PM, Krzyzanowski, Michelle <[hidden email]> wrote:

The Perl prerequisites step is failing, but every other step works.  I have attached the setup.log file.

 

Legacy scripts wig-to-json.pl and bam-to-json.pl have removed from setup. Their functionality has been superseded by add-bam-track.pl and add-bw-track.pl. If you require the old versions, run 'setup.sh legacy'.

Installing javascript dependencies ...Detected precompiled version.

done

Gathering system information ...done

Installing Perl prerequisites ... failed.  See setup.log file for error messages. As a first troubleshooting step, make sure development libraries and header files for GD, Zlib, and libpng are installed and try again.

 

Formatting Volvox example data ... done.

To see the volvox example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/volvox.

 

Formatting Yeast example data ... done.

To see the yeast example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/yeast.

Legacy scripts wig-to-json.pl and bam-to-json.pl have removed from setup. Their functionality has been superseded by add-bam-track.pl and add-bw-track.pl. If you require the old versions, run 'setup.sh legacy'.

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 


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Ontario Institute for Cancer Research



 

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Ontario Institute for Cancer Research



 

--

------------------------------------------------------------------------
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Ontario Institute for Cancer Research


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Re: Using only tracks

Krzyzanowski, Michelle

So then how my colleague set up the tracks is not correct?  Currently, they are hosted on Amazon S3, so I had added them in using data/tracks.conf per the documention.

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

919-485-5648

 

From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, June 06, 2017 2:34 PM
To: Krzyzanowski, Michelle <[hidden email]>
Cc: [hidden email]
Subject: Re: [Gmod-ajax] Using only tracks

 

Thanks Michelle,

 

For supporting multiple organisms, you might want to be aware of this going forward:

 

 

Basically, you'll want a separate directory for each organism, with their own trackList.json files.  Thinking about that before you start putting in a bunch of data that you'll then want to reorganize is a good idea :-)

 

 

Scott

 

 

On Tue, Jun 6, 2017 at 2:23 PM, Krzyzanowski, Michelle <[hidden email]> wrote:

Hi Scott,

 

The website uses SilverStripe for the CMS.

 

We will likely need to support both human and mouse in the future.

 

I am kicking the tires.  No one else here has experience integrating a genome browser.  The PM had told another colleague to create the tracks, thinking it could be used by JBrowse.

 

I am not sure about any other specialty items.

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 

From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, June 06, 2017 2:20 PM
To: Krzyzanowski, Michelle <[hidden email]>
Cc: [hidden email]
Subject: Re: [Gmod-ajax] Using only tracks

 

Hi Michelle,

 

Would it be possible to take a step back and give us an overview of what you are trying to do?  I feel a little like the blind men and the elephant (https://en.wikipedia.org/wiki/Blind_men_and_an_elephant) as we try to help you solve particular pieces, whereas it might be a better use of everyone's time if we knew what you're trying to do.  Items that might help:

 

* what is the nature of the CMS you're working with?  Something built in house or from the outside world (like Drupal)?  What is the javascript infrastructure like (JQuery or the like, for example)?

 

* Do you need to support more than one organism?

 

* Have you been mandated to use JBrowse or are you just kicking the tires? (I ask this because of your reference to track hubs, which is a UCSC genome browser thing, not a JBrowse thing.)

 

* Are there any other "specialty" items that you will need JBrowse to do?  (I realize this is vague and so you may not know the answer.)

 

Thanks,

Scott

 

 

On Tue, Jun 6, 2017 at 1:28 PM, Krzyzanowski, Michelle <[hidden email]> wrote:

For now, I am using a iframe, but am trying to use our own tracks.

 

Another colleague set up the tracks according to this website:

 

http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html

 

I have two questions:

 

1.       How do I get it to not include the volvox sample data

2.      Are the bigwig files as made through the link above compatible with JBrowse?

 

Thank you.

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 

From: Ben Bimber [mailto:[hidden email]]
Sent: Tuesday, June 06, 2017 12:51 PM
To: Nathan Dunn <[hidden email]>
Cc: Scott Cain <[hidden email]>; [hidden email]; Krzyzanowski, Michelle <[hidden email]>
Subject: Re: [Gmod-ajax] Incorporate JBrowse into CMS

 

Sure.  I'll put together a quick demo on one of our public sites and try to write up some more about how it works.  

 

 

On Tue, Jun 6, 2017 at 9:44 AM, Nathan Dunn <[hidden email]> wrote:

 

There is also this PR written by Colin that attempts to do this with Drupal / Tripal.   

 

 

He was able to work around a lot of the css collision issues, by properly scoping (if that’s the word I want) the CSS.  It has the advantage that they are already using dojo, so there didn’t seem to be as many collisions issues with the JS there.    The Apollo project ends up using iFrames, though to avoid multiple collisions issues.

 

Ben,

 

If you have a demo or source-code for how you did that integration, I think many people would be interested (including myself). 

 

Nathan

 

On Jun 6, 2017, at 8:50 AM, Ben Bimber <[hidden email]> wrote:

 

Hello,

 

It sounds like your goal is integration w/ an established CMS; however, a while ago I wrote a module for LabKey Server (https://www.labkey.org), a fairly widely used platform for managing scientific data.  The module is part of DISCVR-Seq (https://github.com/bbimber/discvr-seq/wiki).  This module essentially wraps JBrowse, such that the user can take genomes and resources managed in LabKey and make custom sessions more or less on the fly (i.e. deal w/ all the backend).  Even if not directly of interest, the way we wrapped the JBrowse app (which actually didnt take very much) might be of interest.  There are not terribly thorough docs on this; however, I can answer questions if anyone is interested.

 

-Ben

 

On Tue, Jun 6, 2017 at 8:15 AM, Scott Cain <[hidden email]> wrote:

Hi Michelle,

 

Directly incorporating JBrowse into other pages can be done in some instances but sorting out conflicts between javascript and css can be quite a hassle.  Many people end up using JBrowse in an iframe, although that doesn't always work in the context of a CMS--it all depends.

 

Scott

 

 

On Tue, Jun 6, 2017 at 11:08 AM, Krzyzanowski, Michelle <[hidden email]> wrote:

I’ll check into that, Scott.

 

I have an entirely different question though.  I need to essentially take index.html and incorporate it into the CMS are website uses.  I have included the basic html and included the css and js, however, nothing shows.  I’m guessing I am going to have to modify some directories. 

 

So the new webpage would be outside of the JBrowse folder.

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 

From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, June 06, 2017 10:27 AM
To: Krzyzanowski, Michelle <[hidden email]>
Cc: Colin <[hidden email]>; [hidden email]
Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

Hi Michelle,

 

I assume you're seeing the same thing I am, which is that every track has a pink box with a 404 not found message.  If you look in the apache error log, you'll find the exact path that JBrowse is looking in for the files that it needs.  Normally, the files in the sample_data directory are where they are "supposed" to be automatically (which is to say, they are there when the JBrowse zip file is unpacked).  The question is, where are those files now?

 

Scott

 

 

On Tue, Jun 6, 2017 at 10:07 AM, Krzyzanowski, Michelle <[hidden email]> wrote:

I apologize.  I am looking at this link:

 

http://54.226.19.179/jbrowse/JBrowse-1.12.3/index.html?data=sample_data%2Fjson%2Fvolvox&loc=ctgA%3A20003..30003&tracks=DNA&highlight=

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 

From: Colin [mailto:[hidden email]]
Sent: Monday, June 05, 2017 10:59 AM
To: Scott Cain <[hidden email]>
Cc: Krzyzanowski, Michelle <[hidden email]>; [hidden email]


Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

Normally running the prepare-refseqs.pl would at least create a "Reference sequence" track on the sidebar, so it is weird that your browser at http://54.226.19.179/jbrowse/JBrowse-1.12.3/ doesn't contain a reference sequence track.

 

Did the setup.sh ever complete without errors? Wondering if maybe the Perl pre-requisites step still didn't finish

 

 

-Colin

 

On Mon, Jun 5, 2017 at 10:33 AM, Scott Cain <[hidden email]> wrote:

Hi Michelle,

 

The prepare-refseqs.pl script only gets the fasta sequence ready to display individual residues in JBrowse.  To get feature tracks, you need to use a source of features, like a GFF file.  If you're following the quick start tutorial, you'll see a command like this:

 

bin/biodb-to-json.pl --conf docs/tutorial/conf_files/volvox.json

 

that configuration file has the information in it for finding the volvox GFF file and what data are in it.

Scott

 

 

On Mon, Jun 5, 2017 at 10:19 AM, Krzyzanowski, Michelle <[hidden email]> wrote:

Here is the url:

 

http://54.226.19.179/jbrowse/JBrowse-1.12.3/index.html?loc=ctgA%3A20003..30003&tracks=&highlight=

 

I was simply using the Volvox test data, so my command was:

 

bin/prepare-refseqs.pl --fasta docs/tutorial/data_files/volvox.fa

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 

From: Colin [mailto:[hidden email]]
Sent: Monday, June 05, 2017 10:04 AM
To: Krzyzanowski, Michelle <[hidden email]>
Cc: Scott Cain <[hidden email]>; [hidden email]


Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

What was your prepare-refseqs command?

 

It is not normally necessary to move refSeqs.json files around or other things like the github issue that you linked there.

 

You can maybe look at http://gmod.org/wiki/JBrowse_FAQ#How_do_I_load_my_genome_as_a_FASTA_file.3F for the "simple overview" of loading the genome

 

-Colin

 

On Mon, Jun 5, 2017 at 8:12 AM, Krzyzanowski, Michelle <[hidden email]> wrote:

Hi Scott,

 

Thank you for that line of code.  It seemed to help.

 

However, I do not see any data.  I attached the screenshot of what JBrowse looks like.  I tried doing this:

 

https://github.com/GMOD/jbrowse/issues/549

 

However, it didn’t fix it.

 

Michelle Krzyzanowski

 

From: Scott Cain [mailto:[hidden email]]
Sent: Friday, June 02, 2017 5:18 PM
To: Krzyzanowski, Michelle <[hidden email]>; [hidden email]


Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

Hi Michelle,

 

Please keep the jbrowse mailing cc'ed so other people can chime in with suggests and the discussion can be archived.

 

The OS matters because different flavors of Linux have different package management systems, of which apt is only one.

 

I suspect it failed because the CPAN system (which installs perl modules) is caching the result from before without checking that there is new stuff that it needs to take into account.  Rather that trying to walk you through cleaning that up, I'd suggest that you install some other packages with apt.  This will install the perl module that the installer is currently tripping one and some others as well.  Do this:

 

  sudo apt-get install libhash-merge-perl libjson-xs-perl libjson-perl liblist-moreutils-perl libperlio-gzip-perl libparse-recdescent-perl liblocal-lib-perl libdb-file-perl libxml-parser-perl libbio-perl-perl

 

(that's all one really long line.)  If it asks you to install other stuff, answer yes.  When that is done running, try the jbrowse setup script again.

 

Scott

 

 

On Fri, Jun 2, 2017 at 3:27 PM, Krzyzanowski, Michelle <[hidden email]> wrote:

Hi Scott,

 

I’m not sure why OS matters since this is on the webserver, not local (unless I’m misunderstanding how to install JBrowse).

 

I conducted the sudo install and it ran, and suggested I also install db5.3-doc, which I also did.  Reran setup.sh and still have the failure.

 

Thank you.

 

Michelle

 

From: Scott Cain [mailto:[hidden email]]
Sent: Friday, June 02, 2017 3:14 PM
To: Krzyzanowski, Michelle <[hidden email]>
Cc: [hidden email]
Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

Hi Michelle,

 

Take a look at this:

 

 

The most immediate problem I think is that you need libexpat (of course, there may be others after you fix this).  You didn't mention what OS you're using--hopefully it's one that uses apt-get.

 

Scott

 

 

On Fri, Jun 2, 2017 at 12:53 PM, Krzyzanowski, Michelle <[hidden email]> wrote:

The Perl prerequisites step is failing, but every other step works.  I have attached the setup.log file.

 

Legacy scripts wig-to-json.pl and bam-to-json.pl have removed from setup. Their functionality has been superseded by add-bam-track.pl and add-bw-track.pl. If you require the old versions, run 'setup.sh legacy'.

Installing javascript dependencies ...Detected precompiled version.

done

Gathering system information ...done

Installing Perl prerequisites ... failed.  See setup.log file for error messages. As a first troubleshooting step, make sure development libraries and header files for GD, Zlib, and libpng are installed and try again.

 

Formatting Volvox example data ... done.

To see the volvox example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/volvox.

 

Formatting Yeast example data ... done.

To see the yeast example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/yeast.

Legacy scripts wig-to-json.pl and bam-to-json.pl have removed from setup. Their functionality has been superseded by add-bam-track.pl and add-bw-track.pl. If you require the old versions, run 'setup.sh legacy'.

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 


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--

------------------------------------------------------------------------
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GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research

 



 

--

------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



 

--

------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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Ontario Institute for Cancer Research



 

--

------------------------------------------------------------------------
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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


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Re: Using only tracks

Scott Cain
Hi Michelle, 

JBrowse doesn't support UCSC track hubs, so no, it's probably not usable by JBrowse.  JBrowse does support remote data files though, where you just have to provide a suitable URL in the configuration.  For example, in WormBase's JBrowse instance, I have a few hundred gigs of modENCODE data for JBrowse in an S3 bucket.

Scott


On Tue, Jun 6, 2017 at 2:36 PM, Krzyzanowski, Michelle <[hidden email]> wrote:

So then how my colleague set up the tracks is not correct?  Currently, they are hosted on Amazon S3, so I had added them in using data/tracks.conf per the documention.

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" value="+19194855648" target="_blank">919-485-5648

 

From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, June 06, 2017 2:34 PM


To: Krzyzanowski, Michelle <[hidden email]>
Cc: [hidden email]
Subject: Re: [Gmod-ajax] Using only tracks

 

Thanks Michelle,

 

For supporting multiple organisms, you might want to be aware of this going forward:

 

 

Basically, you'll want a separate directory for each organism, with their own trackList.json files.  Thinking about that before you start putting in a bunch of data that you'll then want to reorganize is a good idea :-)

 

 

Scott

 

 

On Tue, Jun 6, 2017 at 2:23 PM, Krzyzanowski, Michelle <[hidden email]> wrote:

Hi Scott,

 

The website uses SilverStripe for the CMS.

 

We will likely need to support both human and mouse in the future.

 

I am kicking the tires.  No one else here has experience integrating a genome browser.  The PM had told another colleague to create the tracks, thinking it could be used by JBrowse.

 

I am not sure about any other specialty items.

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 

From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, June 06, 2017 2:20 PM
To: Krzyzanowski, Michelle <[hidden email]>
Cc: [hidden email]
Subject: Re: [Gmod-ajax] Using only tracks

 

Hi Michelle,

 

Would it be possible to take a step back and give us an overview of what you are trying to do?  I feel a little like the blind men and the elephant (https://en.wikipedia.org/wiki/Blind_men_and_an_elephant) as we try to help you solve particular pieces, whereas it might be a better use of everyone's time if we knew what you're trying to do.  Items that might help:

 

* what is the nature of the CMS you're working with?  Something built in house or from the outside world (like Drupal)?  What is the javascript infrastructure like (JQuery or the like, for example)?

 

* Do you need to support more than one organism?

 

* Have you been mandated to use JBrowse or are you just kicking the tires? (I ask this because of your reference to track hubs, which is a UCSC genome browser thing, not a JBrowse thing.)

 

* Are there any other "specialty" items that you will need JBrowse to do?  (I realize this is vague and so you may not know the answer.)

 

Thanks,

Scott

 

 

On Tue, Jun 6, 2017 at 1:28 PM, Krzyzanowski, Michelle <[hidden email]> wrote:

For now, I am using a iframe, but am trying to use our own tracks.

 

Another colleague set up the tracks according to this website:

 

http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html

 

I have two questions:

 

1.       How do I get it to not include the volvox sample data

2.      Are the bigwig files as made through the link above compatible with JBrowse?

 

Thank you.

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 

From: Ben Bimber [mailto:[hidden email]]
Sent: Tuesday, June 06, 2017 12:51 PM
To: Nathan Dunn <[hidden email]>
Cc: Scott Cain <[hidden email]>; [hidden email]; Krzyzanowski, Michelle <[hidden email]>
Subject: Re: [Gmod-ajax] Incorporate JBrowse into CMS

 

Sure.  I'll put together a quick demo on one of our public sites and try to write up some more about how it works.  

 

 

On Tue, Jun 6, 2017 at 9:44 AM, Nathan Dunn <[hidden email]> wrote:

 

There is also this PR written by Colin that attempts to do this with Drupal / Tripal.   

 

 

He was able to work around a lot of the css collision issues, by properly scoping (if that’s the word I want) the CSS.  It has the advantage that they are already using dojo, so there didn’t seem to be as many collisions issues with the JS there.    The Apollo project ends up using iFrames, though to avoid multiple collisions issues.

 

Ben,

 

If you have a demo or source-code for how you did that integration, I think many people would be interested (including myself). 

 

Nathan

 

On Jun 6, 2017, at 8:50 AM, Ben Bimber <[hidden email]> wrote:

 

Hello,

 

It sounds like your goal is integration w/ an established CMS; however, a while ago I wrote a module for LabKey Server (https://www.labkey.org), a fairly widely used platform for managing scientific data.  The module is part of DISCVR-Seq (https://github.com/bbimber/discvr-seq/wiki).  This module essentially wraps JBrowse, such that the user can take genomes and resources managed in LabKey and make custom sessions more or less on the fly (i.e. deal w/ all the backend).  Even if not directly of interest, the way we wrapped the JBrowse app (which actually didnt take very much) might be of interest.  There are not terribly thorough docs on this; however, I can answer questions if anyone is interested.

 

-Ben

 

On Tue, Jun 6, 2017 at 8:15 AM, Scott Cain <[hidden email]> wrote:

Hi Michelle,

 

Directly incorporating JBrowse into other pages can be done in some instances but sorting out conflicts between javascript and css can be quite a hassle.  Many people end up using JBrowse in an iframe, although that doesn't always work in the context of a CMS--it all depends.

 

Scott

 

 

On Tue, Jun 6, 2017 at 11:08 AM, Krzyzanowski, Michelle <[hidden email]> wrote:

I’ll check into that, Scott.

 

I have an entirely different question though.  I need to essentially take index.html and incorporate it into the CMS are website uses.  I have included the basic html and included the css and js, however, nothing shows.  I’m guessing I am going to have to modify some directories. 

 

So the new webpage would be outside of the JBrowse folder.

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 

From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, June 06, 2017 10:27 AM
To: Krzyzanowski, Michelle <[hidden email]>
Cc: Colin <[hidden email]>; [hidden email]
Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

Hi Michelle,

 

I assume you're seeing the same thing I am, which is that every track has a pink box with a 404 not found message.  If you look in the apache error log, you'll find the exact path that JBrowse is looking in for the files that it needs.  Normally, the files in the sample_data directory are where they are "supposed" to be automatically (which is to say, they are there when the JBrowse zip file is unpacked).  The question is, where are those files now?

 

Scott

 

 

On Tue, Jun 6, 2017 at 10:07 AM, Krzyzanowski, Michelle <[hidden email]> wrote:

I apologize.  I am looking at this link:

 

http://54.226.19.179/jbrowse/JBrowse-1.12.3/index.html?data=sample_data%2Fjson%2Fvolvox&loc=ctgA%3A20003..30003&tracks=DNA&highlight=

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 

From: Colin [mailto:[hidden email]]
Sent: Monday, June 05, 2017 10:59 AM
To: Scott Cain <[hidden email]>
Cc: Krzyzanowski, Michelle <[hidden email]>; [hidden email]


Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

Normally running the prepare-refseqs.pl would at least create a "Reference sequence" track on the sidebar, so it is weird that your browser at http://54.226.19.179/jbrowse/JBrowse-1.12.3/ doesn't contain a reference sequence track.

 

Did the setup.sh ever complete without errors? Wondering if maybe the Perl pre-requisites step still didn't finish

 

 

-Colin

 

On Mon, Jun 5, 2017 at 10:33 AM, Scott Cain <[hidden email]> wrote:

Hi Michelle,

 

The prepare-refseqs.pl script only gets the fasta sequence ready to display individual residues in JBrowse.  To get feature tracks, you need to use a source of features, like a GFF file.  If you're following the quick start tutorial, you'll see a command like this:

 

bin/biodb-to-json.pl --conf docs/tutorial/conf_files/volvox.json

 

that configuration file has the information in it for finding the volvox GFF file and what data are in it.

Scott

 

 

On Mon, Jun 5, 2017 at 10:19 AM, Krzyzanowski, Michelle <[hidden email]> wrote:

Here is the url:

 

http://54.226.19.179/jbrowse/JBrowse-1.12.3/index.html?loc=ctgA%3A20003..30003&tracks=&highlight=

 

I was simply using the Volvox test data, so my command was:

 

bin/prepare-refseqs.pl --fasta docs/tutorial/data_files/volvox.fa

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 

From: Colin [mailto:[hidden email]]
Sent: Monday, June 05, 2017 10:04 AM
To: Krzyzanowski, Michelle <[hidden email]>
Cc: Scott Cain <[hidden email]>; [hidden email]


Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

What was your prepare-refseqs command?

 

It is not normally necessary to move refSeqs.json files around or other things like the github issue that you linked there.

 

You can maybe look at http://gmod.org/wiki/JBrowse_FAQ#How_do_I_load_my_genome_as_a_FASTA_file.3F for the "simple overview" of loading the genome

 

-Colin

 

On Mon, Jun 5, 2017 at 8:12 AM, Krzyzanowski, Michelle <[hidden email]> wrote:

Hi Scott,

 

Thank you for that line of code.  It seemed to help.

 

However, I do not see any data.  I attached the screenshot of what JBrowse looks like.  I tried doing this:

 

https://github.com/GMOD/jbrowse/issues/549

 

However, it didn’t fix it.

 

Michelle Krzyzanowski

 

From: Scott Cain [mailto:[hidden email]]
Sent: Friday, June 02, 2017 5:18 PM
To: Krzyzanowski, Michelle <[hidden email]>; [hidden email]


Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

Hi Michelle,

 

Please keep the jbrowse mailing cc'ed so other people can chime in with suggests and the discussion can be archived.

 

The OS matters because different flavors of Linux have different package management systems, of which apt is only one.

 

I suspect it failed because the CPAN system (which installs perl modules) is caching the result from before without checking that there is new stuff that it needs to take into account.  Rather that trying to walk you through cleaning that up, I'd suggest that you install some other packages with apt.  This will install the perl module that the installer is currently tripping one and some others as well.  Do this:

 

  sudo apt-get install libhash-merge-perl libjson-xs-perl libjson-perl liblist-moreutils-perl libperlio-gzip-perl libparse-recdescent-perl liblocal-lib-perl libdb-file-perl libxml-parser-perl libbio-perl-perl

 

(that's all one really long line.)  If it asks you to install other stuff, answer yes.  When that is done running, try the jbrowse setup script again.

 

Scott

 

 

On Fri, Jun 2, 2017 at 3:27 PM, Krzyzanowski, Michelle <[hidden email]> wrote:

Hi Scott,

 

I’m not sure why OS matters since this is on the webserver, not local (unless I’m misunderstanding how to install JBrowse).

 

I conducted the sudo install and it ran, and suggested I also install db5.3-doc, which I also did.  Reran setup.sh and still have the failure.

 

Thank you.

 

Michelle

 

From: Scott Cain [mailto:[hidden email]]
Sent: Friday, June 02, 2017 3:14 PM
To: Krzyzanowski, Michelle <[hidden email]>
Cc: [hidden email]
Subject: Re: [Gmod-ajax] JBrowse SetUp Error

 

Hi Michelle,

 

Take a look at this:

 

 

The most immediate problem I think is that you need libexpat (of course, there may be others after you fix this).  You didn't mention what OS you're using--hopefully it's one that uses apt-get.

 

Scott

 

 

On Fri, Jun 2, 2017 at 12:53 PM, Krzyzanowski, Michelle <[hidden email]> wrote:

The Perl prerequisites step is failing, but every other step works.  I have attached the setup.log file.

 

Legacy scripts wig-to-json.pl and bam-to-json.pl have removed from setup. Their functionality has been superseded by add-bam-track.pl and add-bw-track.pl. If you require the old versions, run 'setup.sh legacy'.

Installing javascript dependencies ...Detected precompiled version.

done

Gathering system information ...done

Installing Perl prerequisites ... failed.  See setup.log file for error messages. As a first troubleshooting step, make sure development libraries and header files for GD, Zlib, and libpng are installed and try again.

 

Formatting Volvox example data ... done.

To see the volvox example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/volvox.

 

Formatting Yeast example data ... done.

To see the yeast example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/yeast.

Legacy scripts wig-to-json.pl and bam-to-json.pl have removed from setup. Their functionality has been superseded by add-bam-track.pl and add-bw-track.pl. If you require the old versions, run 'setup.sh legacy'.

 

Michelle Krzyzanowski

Research Computing Division

RTI International

[hidden email]

<a href="tel:(919)%20485-5648" target="_blank">919-485-5648

 


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Scott Cain, Ph. D.                                   scott at scottcain dot net
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Ontario Institute for Cancer Research



 

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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research

 



 

--

------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



 

--

------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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--

------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



 

--

------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" target="_blank">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

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