Re: Incorporate JBrowse into CMS

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Re: Incorporate JBrowse into CMS

Krzyzanowski, Michelle

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]

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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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/)                     216-392-3087
Ontario Institute for Cancer Research


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Re: Incorporate JBrowse into CMS

Scott Cain
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" value="+19194855648" 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
_______________________________________________
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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


------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
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" 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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Re: Incorporate JBrowse into CMS

Ben Bimber
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" value="+19194855648" 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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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/)                     <a href="tel:(216)%20392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research

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Re: Incorporate JBrowse into CMS

nathandunn

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" value="+19194855648" target="_blank" class="">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" class="">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" class="">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" class="">919-485-5648

 


------------------------------------------------------------------------------
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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" class="">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" class="">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" class="">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" class="">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" class="">216-392-3087
Ontario Institute for Cancer Research

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Re: Incorporate JBrowse into CMS

Ben Bimber
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" value="+19194855648" 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: Incorporate JBrowse into CMS

Mts Mft
In reply to this post by Krzyzanowski, Michelle
Hi Michelle K.,

So the easiest I found to "integrate" JBrowse with our CMS (wordpress) is to keep JBrowse instances outside the CMS and serves existing directories before the CMS itself.
In case of wordpress, it implies using the URL rewriting that happen in the .htaccess file at the CMS root. This file redirect everything to the wordpress index.php file and do some blackbox PHP magic.
If you have access to your server config:

1- Serve the server root (<ROOT>)

2- Redirect all your trafic to the directory in which your CMS is located e.g. at <ROOT>/my_cms, which mean you can access the website normally using www.mywebsite.com

3- Have different 
JBrowse instances in their own directory at root e.g. <ROOT>/jbrowse1<ROOT>/jbrowse2

The key point in the set-up is to serve an existing directory at root if it exist (1)
and if it doenst let the CMS do the magic (2)

(1) e.g. <ROOT>/jbrowse1 will be serve from www.mywebsite.com/jbrowse1 because it exists.
(2) Accessing
www.mywebsite.com/non_existing_jbrowse will let the CMS decide what to serve using "non_existing_jbrowse" (most probably 404 not found)
(2) Accessing www.mywebsite.com/my_cms_page1 will access my_cms_page1 if it exists; if it doesn't: 404 not found

Cheers,

M.


Le 06/06/17 à 17:08, Krzyzanowski, Michelle a écrit :

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]

919-485-5648

 

From: Scott Cain [[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 moz-do-not-send="true" href="tel:%28919%29%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 moz-do-not-send="true" href="tel:%28919%29%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 moz-do-not-send="true" href="tel:%28919%29%20485-5648" target="_blank">919-485-5648

 


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Ontario Institute for Cancer Research



 

--

------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a moz-do-not-send="true" href="tel:%28216%29%20392-3087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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GMOD Coordinator (http://gmod.org/)                     <a moz-do-not-send="true" href="tel:%28216%29%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/)                     216-392-3087
Ontario Institute for Cancer Research



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