[Gmod-ajax] Remote .fa files

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[Gmod-ajax] Remote .fa files

Krzyzanowski, Michelle

Hi Scott and all,

 

Now I have the correct files to work with, I have both .fa and .gtf files.  I was reading the wiki, and it mentions running bin/prepare-refseqs.pl --fasta your_genome.fa with the .fa file in the directory itself. 

 

I would rather keep the .fa and .gtf files on Amazon S3.  Could I simply conduct the same process by using the full url of where the files are located?  I’m trying to run the command, but it is giving me an error:

 

bin/prepare-refseqs.pl --fasta [external url to cloud]/Mus_musculus.GRCm38.dna.chromosome.1.fa --out LMEX0000001224

 

Would this also be possible with the gff file? I.e. this command:

 

bin/flatfile-to-json.pl --gff myfile.gff --trackLabel trackLabel

 

 

Finally, I have .fa files for each chromosome in mouse.  Will JBrowse automatically set up a  dropdown to switch among chromosomes?

 

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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--

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


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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



 

--

------------------------------------------------------------------------
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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Re: Remote .fa files

Keiran Raine

Hi,

 

You may want to use an indexed fasta file 'samtools faidx' instead, it can also be compressed.

 

Just a warning, but be aware of egress charges when hosting data on Amazon S3.  See 'Request Pricing': https://aws.amazon.com/s3/pricing/

 

Remember that JBrowse will do thousands of requests against the files as it is range/chunk requested.

 

Regards,

 

Keiran Raine

Principal Bioinformatician

Cancer Genome Project

Wellcome Trust Sanger Institute

 

[hidden email]

Tel:+44 (0)1223 834244 Ext: 4983

Office: H104

 

From: "Krzyzanowski, Michelle" <[hidden email]>
Date: Tuesday, 13 June 2017 at 19:53
To: Scott Cain <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Subject: [Gmod-ajax] Remote .fa files

 

Hi Scott and all,

 

Now I have the correct files to work with, I have both .fa and .gtf files.  I was reading the wiki, and it mentions running bin/prepare-refseqs.pl --fasta your_genome.fa with the .fa file in the directory itself. 

 

I would rather keep the .fa and .gtf files on Amazon S3.  Could I simply conduct the same process by using the full url of where the files are located?  I’m trying to run the command, but it is giving me an error:

 

bin/prepare-refseqs.pl --fasta [external url to cloud]/Mus_musculus.GRCm38.dna.chromosome.1.fa --out LMEX0000001224

 

Would this also be possible with the gff file? I.e. this command:

 

bin/flatfile-to-json.pl --gff myfile.gff --trackLabel trackLabel

 

 

Finally, I have .fa files for each chromosome in mouse.  Will JBrowse automatically set up a  dropdown to switch among chromosomes?

 

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

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Re: Remote .fa files

Scott Cain
Hi Michelle,

Keiran's warning is a good one: S3 charges per GET in addition to bandwidth charges, of which JBrowse generates quite a few.  On the other hand, the charge per GET is quite small, so the only way to know if it's financially doable is to do it.

The data prep tools don't have a built in way to access remote file systems.  What I would suggest doing is getting everything set up on a local server and get it configured the way you want and then transfer the data to S3.

I've written a few scripts that can help with that here:

  https://github.com/alliance-genome/jbrowse-config/tree/master/scripts

The upload_to_S3.pl script copies the track, sequence and name data to an S3 bucket, sets the access permissions both on the individual files, the bucket as a whole and sets CORS so that javascript requests from a jbrowse instance on a different server will be allowed.

The upload_jbrowse_static.pl script copies all of the other stuff that JBrowse needs to run.  I did this as a separate script because it is not unreasonable to want to put the JBrowse track data in an S3 bucket but serve JBrowse from an apache instance.  It is possible to put everything for JBrowse in one bucket but you just would have to be careful with what path to use when transferring your track data so that it is consistent with what JBrowse expects when you upload the configuration files (trackList.json).

Finally, a fairly simple example of JBrowse running with S3 for track data and apache for the JBrowse files is at

  http://jbrowse.alliancegenome.org/jbrowse/

Finally, here's one useful hint for developing a JBrowse instance: since JBrowse is entirely client-side, all of the configuration files for a JBrowse instance are available to the web browser directly.  For instance, if I wanted to see how I set up the trackList.json file for the C. elegans browser at alliancegenome.org, I could just point my browser at

  http://jbrowse.alliancegenome.org/jbrowse/data/Caenorhabditis%20elegans/trackList.json

to get it.  You can figure that URL from looking at the javascript console for files that JBrowse requests when it's loading the page.

Good luck,
Scott


On Wed, Jun 14, 2017 at 4:48 AM, Keiran Raine <[hidden email]> wrote:

Hi,

 

You may want to use an indexed fasta file 'samtools faidx' instead, it can also be compressed.

 

Just a warning, but be aware of egress charges when hosting data on Amazon S3.  See 'Request Pricing': https://aws.amazon.com/s3/pricing/

 

Remember that JBrowse will do thousands of requests against the files as it is range/chunk requested.

 

Regards,

 

Keiran Raine

Principal Bioinformatician

Cancer Genome Project

Wellcome Trust Sanger Institute

 

[hidden email]

Tel:<a href="tel:+44%201223%20834244" value="+441223834244" target="_blank">+44 (0)1223 834244 Ext: 4983

Office: H104

 

From: "Krzyzanowski, Michelle" <[hidden email]>
Date: Tuesday, 13 June 2017 at 19:53
To: Scott Cain <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Subject: [Gmod-ajax] Remote .fa files

 

Hi Scott and all,

 

Now I have the correct files to work with, I have both .fa and .gtf files.  I was reading the wiki, and it mentions running bin/prepare-refseqs.pl --fasta your_genome.fa with the .fa file in the directory itself. 

 

I would rather keep the .fa and .gtf files on Amazon S3.  Could I simply conduct the same process by using the full url of where the files are located?  I’m trying to run the command, but it is giving me an error:

 

bin/prepare-refseqs.pl --fasta [external url to cloud]/Mus_musculus.GRCm38.dna.chromosome.1.fa --out LMEX0000001224

 

Would this also be possible with the gff file? I.e. this command:

 

bin/flatfile-to-json.pl --gff myfile.gff --trackLabel trackLabel

 

 

Finally, I have .fa files for each chromosome in mouse.  Will JBrowse automatically set up a  dropdown to switch among chromosomes?

 

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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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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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

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



--
------------------------------------------------------------------------
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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