[Gmod-ajax] Using multiple "data" directories with a single copy of JBrowse code (from July 2010 post)

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[Gmod-ajax] Using multiple "data" directories with a single copy of JBrowse code (from July 2010 post)

mmacd
Hi everyone,
I just started working with JBrowse a few weeks ago and am having some issues with adding multiple references/datasets. I saw that there was a post in July 2010 concerning the issue with multiple data set directories (http://gmod.827538.n3.nabble.com/Gmod-ajax-Using-multiple-quot-data-quot-directories-with-a-single-copy-of-JBrowse-code-td985629.html#none). 

I was wondering how to do the same thing but with the most recent version of JBrowse. The index.html file is different now than in the 2010 version, and this is where I am getting stuck in adding multiple data directories. Any help is appreciated!
Thank you,
Maddy MacDonald

--
Madolyn MacDonald
UDel Bioinformatics and Systems Biology, PhD student
RIT Alumnus 13'

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Re: Using multiple "data" directories with a single copy of JBrowse code (from July 2010 post)

Scott Cain
Hi Madolyn,

I think this is what you need:


Scott



On Wed, Mar 12, 2014 at 3:09 PM, Madolyn Macdonald <[hidden email]> wrote:
Hi everyone,
I just started working with JBrowse a few weeks ago and am having some issues with adding multiple references/datasets. I saw that there was a post in July 2010 concerning the issue with multiple data set directories (http://gmod.827538.n3.nabble.com/Gmod-ajax-Using-multiple-quot-data-quot-directories-with-a-single-copy-of-JBrowse-code-td985629.html#none). 

I was wondering how to do the same thing but with the most recent version of JBrowse. The index.html file is different now than in the 2010 version, and this is where I am getting stuck in adding multiple data directories. Any help is appreciated!
Thank you,
Maddy MacDonald

--
Madolyn MacDonald
UDel Bioinformatics and Systems Biology, PhD student
RIT Alumnus 13'

------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/13534_NeoTech
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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Using multiple "data" directories with a single copy of JBrowse code (from July 2010 post)

mmacd
Hi Scott,
I completed the instructions from that link and can see the data selector menu on my instance, but now I am at the point of adding the reference sequences for my different datasets. I am getting multiple trackList.jsn files and seq folders after using the prepare reference sequences scripts, and I need to keep them in different directories. Unless there is a way to combine them?
 
I am trying to view multiple chromosomes in one JBrowse instance, each which have multiple scaffolds. I currently have one chromosome working, but would now like to add the others under the data set selector.  

Thank you!


On Wed, Mar 12, 2014 at 4:46 PM, Scott Cain <[hidden email]> wrote:
Hi Madolyn,

I think this is what you need:


Scott



On Wed, Mar 12, 2014 at 3:09 PM, Madolyn Macdonald <[hidden email]> wrote:
Hi everyone,
I just started working with JBrowse a few weeks ago and am having some issues with adding multiple references/datasets. I saw that there was a post in July 2010 concerning the issue with multiple data set directories (http://gmod.827538.n3.nabble.com/Gmod-ajax-Using-multiple-quot-data-quot-directories-with-a-single-copy-of-JBrowse-code-td985629.html#none). 

I was wondering how to do the same thing but with the most recent version of JBrowse. The index.html file is different now than in the 2010 version, and this is where I am getting stuck in adding multiple data directories. Any help is appreciated!
Thank you,
Maddy MacDonald

--
Madolyn MacDonald
UDel Bioinformatics and Systems Biology, PhD student
RIT Alumnus 13'

------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/13534_NeoTech
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------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
Madolyn MacDonald
UDel Bioinformatics and Systems Biology, PhD student
RIT Alumnus 13'

------------------------------------------------------------------------------
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"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
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Re: Using multiple "data" directories with a single copy of JBrowse code (from July 2010 post)

Scott Cain
Hi Madolyn,

I'm not sure I understand: do you have more than one organism? If not, then typically, you wouldn't use the data set selector, and wouldn't use more than one data directory.

Scott





On Wed, Mar 12, 2014 at 5:04 PM, Madolyn Macdonald <[hidden email]> wrote:
Hi Scott,
I completed the instructions from that link and can see the data selector menu on my instance, but now I am at the point of adding the reference sequences for my different datasets. I am getting multiple trackList.jsn files and seq folders after using the prepare reference sequences scripts, and I need to keep them in different directories. Unless there is a way to combine them?
 
I am trying to view multiple chromosomes in one JBrowse instance, each which have multiple scaffolds. I currently have one chromosome working, but would now like to add the others under the data set selector.  

Thank you!


On Wed, Mar 12, 2014 at 4:46 PM, Scott Cain <[hidden email]> wrote:
Hi Madolyn,

I think this is what you need:


Scott



On Wed, Mar 12, 2014 at 3:09 PM, Madolyn Macdonald <[hidden email]> wrote:
Hi everyone,
I just started working with JBrowse a few weeks ago and am having some issues with adding multiple references/datasets. I saw that there was a post in July 2010 concerning the issue with multiple data set directories (http://gmod.827538.n3.nabble.com/Gmod-ajax-Using-multiple-quot-data-quot-directories-with-a-single-copy-of-JBrowse-code-td985629.html#none). 

I was wondering how to do the same thing but with the most recent version of JBrowse. The index.html file is different now than in the 2010 version, and this is where I am getting stuck in adding multiple data directories. Any help is appreciated!
Thank you,
Maddy MacDonald

--
Madolyn MacDonald
UDel Bioinformatics and Systems Biology, PhD student
RIT Alumnus 13'

------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/13534_NeoTech
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
Madolyn MacDonald
UDel Bioinformatics and Systems Biology, PhD student
RIT Alumnus 13'



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

------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
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applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/13534_NeoTech
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Re: Using multiple "data" directories with a single copy of JBrowse code (from July 2010 post)

mmacd
I don't have multiple organisms, just one organism with 11 chromosomes. I have a fasta file for each chromosome each containing multiple scaffold sequences so I have to run the prepare ref sequences script multiple times, correct? I want to keep the chromosomes separated. Each chromosome is made up of many scaffolds as the assembly is still under construction and these are listed in the pull down menu next to the zoom in button (not the chromosomes).
Sorry, it is difficult to explain!


On Wed, Mar 12, 2014 at 6:14 PM, Scott Cain <[hidden email]> wrote:
Hi Madolyn,

I'm not sure I understand: do you have more than one organism? If not, then typically, you wouldn't use the data set selector, and wouldn't use more than one data directory.

Scott





On Wed, Mar 12, 2014 at 5:04 PM, Madolyn Macdonald <[hidden email]> wrote:
Hi Scott,
I completed the instructions from that link and can see the data selector menu on my instance, but now I am at the point of adding the reference sequences for my different datasets. I am getting multiple trackList.jsn files and seq folders after using the prepare reference sequences scripts, and I need to keep them in different directories. Unless there is a way to combine them?
 
I am trying to view multiple chromosomes in one JBrowse instance, each which have multiple scaffolds. I currently have one chromosome working, but would now like to add the others under the data set selector.  

Thank you!


On Wed, Mar 12, 2014 at 4:46 PM, Scott Cain <[hidden email]> wrote:
Hi Madolyn,

I think this is what you need:


Scott



On Wed, Mar 12, 2014 at 3:09 PM, Madolyn Macdonald <[hidden email]> wrote:
Hi everyone,
I just started working with JBrowse a few weeks ago and am having some issues with adding multiple references/datasets. I saw that there was a post in July 2010 concerning the issue with multiple data set directories (http://gmod.827538.n3.nabble.com/Gmod-ajax-Using-multiple-quot-data-quot-directories-with-a-single-copy-of-JBrowse-code-td985629.html#none). 

I was wondering how to do the same thing but with the most recent version of JBrowse. The index.html file is different now than in the 2010 version, and this is where I am getting stuck in adding multiple data directories. Any help is appreciated!
Thank you,
Maddy MacDonald

--
Madolyn MacDonald
UDel Bioinformatics and Systems Biology, PhD student
RIT Alumnus 13'

------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/13534_NeoTech
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
Madolyn MacDonald
UDel Bioinformatics and Systems Biology, PhD student
RIT Alumnus 13'



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
Madolyn MacDonald
UDel Bioinformatics and Systems Biology, PhD student
RIT Alumnus 13'

------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/13534_NeoTech
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Re: Using multiple "data" directories with a single copy of JBrowse code (from July 2010 post)

Colin
Hi Madolyn,
I think using multiple data directories is a possibility for your use case, but the June 2010 thread is pretty outdated. The link that Scott Cain had is much more up to date about using multiple data directories, and you can see this type of configuration in action with the sample_data examples (volvox,modencode,etc). IMO, one of the problems currently is that the refseq dropdown menu is limited, especially with many scaffolds, so in the future we might add more functionality.


-Colin




On Thu, Mar 13, 2014 at 9:15 AM, Madolyn Macdonald <[hidden email]> wrote:
I don't have multiple organisms, just one organism with 11 chromosomes. I have a fasta file for each chromosome each containing multiple scaffold sequences so I have to run the prepare ref sequences script multiple times, correct? I want to keep the chromosomes separated. Each chromosome is made up of many scaffolds as the assembly is still under construction and these are listed in the pull down menu next to the zoom in button (not the chromosomes).
Sorry, it is difficult to explain!


On Wed, Mar 12, 2014 at 6:14 PM, Scott Cain <[hidden email]> wrote:
Hi Madolyn,

I'm not sure I understand: do you have more than one organism? If not, then typically, you wouldn't use the data set selector, and wouldn't use more than one data directory.

Scott





On Wed, Mar 12, 2014 at 5:04 PM, Madolyn Macdonald <[hidden email]> wrote:
Hi Scott,
I completed the instructions from that link and can see the data selector menu on my instance, but now I am at the point of adding the reference sequences for my different datasets. I am getting multiple trackList.jsn files and seq folders after using the prepare reference sequences scripts, and I need to keep them in different directories. Unless there is a way to combine them?
 
I am trying to view multiple chromosomes in one JBrowse instance, each which have multiple scaffolds. I currently have one chromosome working, but would now like to add the others under the data set selector.  

Thank you!


On Wed, Mar 12, 2014 at 4:46 PM, Scott Cain <[hidden email]> wrote:
Hi Madolyn,

I think this is what you need:


Scott



On Wed, Mar 12, 2014 at 3:09 PM, Madolyn Macdonald <[hidden email]> wrote:
Hi everyone,
I just started working with JBrowse a few weeks ago and am having some issues with adding multiple references/datasets. I saw that there was a post in July 2010 concerning the issue with multiple data set directories (http://gmod.827538.n3.nabble.com/Gmod-ajax-Using-multiple-quot-data-quot-directories-with-a-single-copy-of-JBrowse-code-td985629.html#none). 

I was wondering how to do the same thing but with the most recent version of JBrowse. The index.html file is different now than in the 2010 version, and this is where I am getting stuck in adding multiple data directories. Any help is appreciated!
Thank you,
Maddy MacDonald

--
Madolyn MacDonald
UDel Bioinformatics and Systems Biology, PhD student
RIT Alumnus 13'

------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/13534_NeoTech
_______________________________________________
Gmod-ajax mailing list
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
Madolyn MacDonald
UDel Bioinformatics and Systems Biology, PhD student
RIT Alumnus 13'



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
Madolyn MacDonald
UDel Bioinformatics and Systems Biology, PhD student
RIT Alumnus 13'

------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/13534_NeoTech
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Re: Using multiple "data" directories with a single copy of JBrowse code (from July 2010 post)

Hans Vasquez-Gross
Hi Madolyn,

   I recently ran into this same problem.  With wheats' large genome, the performance on JBrowse was too slow for the full reference.  I had to split up each chromosome as a separate dataset.

Example:

You will notice in the dataset selector each chromosome arm has has their own option.  The steps to do this are as follows:

  1. I created separate fasta files for each logical dataset
  2. Ran the prepare refseqs command then moved the files in the appropriate directory.
    time bin/prepare-refseqs.pl --fasta /Volumes/DATA2/users/havasquezgross/Projects/exon_capture/database/iwgsc-split/IWGSC_CSS_AB-TGAC_v1.ref1AS.fa
    mv data/seq/ data/json/iwgsc-1AS
    mv data/track* data/json/iwgsc-1AS


  3. Edit the tracks.conf file and add the NEEDED dataset name.  Include any other tracks here too (vcf, bams, gff3 annotations, etc)
    [general]
    dataset_id = iwgsc-1AS


  4. Generate names for the individual dataset:
    time bin/generate-names.pl --verbose --out data/json/iwgsc-1AS/

  5. Edit the main jbrowse.conf and add the dataset at the bottom.
    [datasets.iwgsc-1AS]
    url  = ?data=data/json/iwgsc-1AS
    name = IWGSC-1AS

  6. You should now be able to see this dataset in the dropdown.  Repeat the same process for each reference file.

I hope this helps.  Let me know if you have any questions.

Cheers,
-Hans


On Thu, Mar 13, 2014 at 11:01 AM, Colin <[hidden email]> wrote:
Hi Madolyn,
I think using multiple data directories is a possibility for your use case, but the June 2010 thread is pretty outdated. The link that Scott Cain had is much more up to date about using multiple data directories, and you can see this type of configuration in action with the sample_data examples (volvox,modencode,etc). IMO, one of the problems currently is that the refseq dropdown menu is limited, especially with many scaffolds, so in the future we might add more functionality.


-Colin




On Thu, Mar 13, 2014 at 9:15 AM, Madolyn Macdonald <[hidden email]> wrote:
I don't have multiple organisms, just one organism with 11 chromosomes. I have a fasta file for each chromosome each containing multiple scaffold sequences so I have to run the prepare ref sequences script multiple times, correct? I want to keep the chromosomes separated. Each chromosome is made up of many scaffolds as the assembly is still under construction and these are listed in the pull down menu next to the zoom in button (not the chromosomes).
Sorry, it is difficult to explain!


On Wed, Mar 12, 2014 at 6:14 PM, Scott Cain <[hidden email]> wrote:
Hi Madolyn,

I'm not sure I understand: do you have more than one organism? If not, then typically, you wouldn't use the data set selector, and wouldn't use more than one data directory.

Scott





On Wed, Mar 12, 2014 at 5:04 PM, Madolyn Macdonald <[hidden email]> wrote:
Hi Scott,
I completed the instructions from that link and can see the data selector menu on my instance, but now I am at the point of adding the reference sequences for my different datasets. I am getting multiple trackList.jsn files and seq folders after using the prepare reference sequences scripts, and I need to keep them in different directories. Unless there is a way to combine them?
 
I am trying to view multiple chromosomes in one JBrowse instance, each which have multiple scaffolds. I currently have one chromosome working, but would now like to add the others under the data set selector.  

Thank you!


On Wed, Mar 12, 2014 at 4:46 PM, Scott Cain <[hidden email]> wrote:
Hi Madolyn,

I think this is what you need:


Scott



On Wed, Mar 12, 2014 at 3:09 PM, Madolyn Macdonald <[hidden email]> wrote:
Hi everyone,
I just started working with JBrowse a few weeks ago and am having some issues with adding multiple references/datasets. I saw that there was a post in July 2010 concerning the issue with multiple data set directories (http://gmod.827538.n3.nabble.com/Gmod-ajax-Using-multiple-quot-data-quot-directories-with-a-single-copy-of-JBrowse-code-td985629.html#none). 

I was wondering how to do the same thing but with the most recent version of JBrowse. The index.html file is different now than in the 2010 version, and this is where I am getting stuck in adding multiple data directories. Any help is appreciated!
Thank you,
Maddy MacDonald

--
Madolyn MacDonald
UDel Bioinformatics and Systems Biology, PhD student
RIT Alumnus 13'

------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/13534_NeoTech
_______________________________________________
Gmod-ajax mailing list
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
Madolyn MacDonald
UDel Bioinformatics and Systems Biology, PhD student
RIT Alumnus 13'



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
Madolyn MacDonald
UDel Bioinformatics and Systems Biology, PhD student
RIT Alumnus 13'

------------------------------------------------------------------------------
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"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
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Hans Vasquez-Gross
Programmer
Dubcovsky and Neale Lab
Department of Plant Science
University of California at Davis
Skype: hansvg.ucd

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Re: Using multiple "data" directories with a single copy of JBrowse code (from July 2010 post)

mmacd
Hi Hans,
I followed your instructions for two of my reference files and am able to see them both in the dataset drop down menu. My first chromosome (chr8) works when I first start up jbrowse and I am able to switch to my second chromosome (chr9_10). However, jbrowse does not show the reference sequence for the second chromosome and I am then also unable to go back to view my first chromosome that was working originally. 

I am thinking it may be the include statements in jbrowse.conf that I am doing wrong. This is what I have:

## edit this include statement to load and merge in more configuration files
include  = {dataRoot}/chr8/trackList.json
include += {dataRoot}/chr8/tracks.conf
include += {dataRoot}/chr9_10/tracks.conf
include += {dataRoot}/chr9_10/trackList.json

[datasets.chr8]
url  = ?data=data/chr8
name = chr8

[datasets.chr9_10]
url = ?data=data/chr9_10
name = chr9_10

The bottom of my jbrowse.conf file looks like:

Any ideas?
Thanks,
Maddy



On Thu, Mar 13, 2014 at 2:27 PM, Hans Vasquez-Gross <[hidden email]> wrote:
Hi Madolyn,

   I recently ran into this same problem.  With wheats' large genome, the performance on JBrowse was too slow for the full reference.  I had to split up each chromosome as a separate dataset.

Example:

You will notice in the dataset selector each chromosome arm has has their own option.  The steps to do this are as follows:

  1. I created separate fasta files for each logical dataset
  2. Ran the prepare refseqs command then moved the files in the appropriate directory.
    time bin/prepare-refseqs.pl --fasta /Volumes/DATA2/users/havasquezgross/Projects/exon_capture/database/iwgsc-split/IWGSC_CSS_AB-TGAC_v1.ref1AS.fa
    mv data/seq/ data/json/iwgsc-1AS
    mv data/track* data/json/iwgsc-1AS


  3. Edit the tracks.conf file and add the NEEDED dataset name.  Include any other tracks here too (vcf, bams, gff3 annotations, etc)
    [general]
    dataset_id = iwgsc-1AS


  4. Generate names for the individual dataset:
    time bin/generate-names.pl --verbose --out data/json/iwgsc-1AS/

  5. Edit the main jbrowse.conf and add the dataset at the bottom.
    [datasets.iwgsc-1AS]
    url  = ?data=data/json/iwgsc-1AS
    name = IWGSC-1AS

  6. You should now be able to see this dataset in the dropdown.  Repeat the same process for each reference file.

I hope this helps.  Let me know if you have any questions.

Cheers,
-Hans


On Thu, Mar 13, 2014 at 11:01 AM, Colin <[hidden email]> wrote:
Hi Madolyn,
I think using multiple data directories is a possibility for your use case, but the June 2010 thread is pretty outdated. The link that Scott Cain had is much more up to date about using multiple data directories, and you can see this type of configuration in action with the sample_data examples (volvox,modencode,etc). IMO, one of the problems currently is that the refseq dropdown menu is limited, especially with many scaffolds, so in the future we might add more functionality.


-Colin




On Thu, Mar 13, 2014 at 9:15 AM, Madolyn Macdonald <[hidden email]> wrote:
I don't have multiple organisms, just one organism with 11 chromosomes. I have a fasta file for each chromosome each containing multiple scaffold sequences so I have to run the prepare ref sequences script multiple times, correct? I want to keep the chromosomes separated. Each chromosome is made up of many scaffolds as the assembly is still under construction and these are listed in the pull down menu next to the zoom in button (not the chromosomes).
Sorry, it is difficult to explain!


On Wed, Mar 12, 2014 at 6:14 PM, Scott Cain <[hidden email]> wrote:
Hi Madolyn,

I'm not sure I understand: do you have more than one organism? If not, then typically, you wouldn't use the data set selector, and wouldn't use more than one data directory.

Scott





On Wed, Mar 12, 2014 at 5:04 PM, Madolyn Macdonald <[hidden email]> wrote:
Hi Scott,
I completed the instructions from that link and can see the data selector menu on my instance, but now I am at the point of adding the reference sequences for my different datasets. I am getting multiple trackList.jsn files and seq folders after using the prepare reference sequences scripts, and I need to keep them in different directories. Unless there is a way to combine them?
 
I am trying to view multiple chromosomes in one JBrowse instance, each which have multiple scaffolds. I currently have one chromosome working, but would now like to add the others under the data set selector.  

Thank you!


On Wed, Mar 12, 2014 at 4:46 PM, Scott Cain <[hidden email]> wrote:
Hi Madolyn,

I think this is what you need:


Scott



On Wed, Mar 12, 2014 at 3:09 PM, Madolyn Macdonald <[hidden email]> wrote:
Hi everyone,
I just started working with JBrowse a few weeks ago and am having some issues with adding multiple references/datasets. I saw that there was a post in July 2010 concerning the issue with multiple data set directories (http://gmod.827538.n3.nabble.com/Gmod-ajax-Using-multiple-quot-data-quot-directories-with-a-single-copy-of-JBrowse-code-td985629.html#none). 

I was wondering how to do the same thing but with the most recent version of JBrowse. The index.html file is different now than in the 2010 version, and this is where I am getting stuck in adding multiple data directories. Any help is appreciated!
Thank you,
Maddy MacDonald

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UDel Bioinformatics and Systems Biology, PhD student
RIT Alumnus 13'

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UDel Bioinformatics and Systems Biology, PhD student
RIT Alumnus 13'



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------------------------------------------------------------------------
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UDel Bioinformatics and Systems Biology, PhD student
RIT Alumnus 13'

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RIT Alumnus 13'

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Re: Using multiple "data" directories with a single copy of JBrowse code (from July 2010 post)

Hans Vasquez-Gross
Hi Madolyn,

Only add the [datasets.] block of codes you included at the bottom of the jbrowse.conf file.  Delete all the include lines you added, those are unneeded and will be included automatically for the specific dataset.  This is what's causing the mixup in JBrowse when you try loading refseqs. 

Do you have a link I can try out?  I can look at the javascript debugging window and maybe find more information out.

Cheers,
-Hans

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Re: Using multiple "data" directories with a single copy of JBrowse code (from July 2010 post)

mmacd
If I delete all the include statements I added, I should have one left, correct? I am not sure what config file I need to use for the first include statement since I have config files for each chromosome. Should I have some type of combined config file for the chromosomes?
If I delete all of the include statements, no data (references or tracks) show up in jbrowse. 


On Fri, Mar 14, 2014 at 1:28 PM, Hans Vasquez-Gross <[hidden email]> wrote:
Hi Madolyn,

Only add the [datasets.] block of codes you included at the bottom of the jbrowse.conf file.  Delete all the include lines you added, those are unneeded and will be included automatically for the specific dataset.  This is what's causing the mixup in JBrowse when you try loading refseqs. 

Do you have a link I can try out?  I can look at the javascript debugging window and maybe find more information out.

Cheers,
-Hans



--
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UDel Bioinformatics and Systems Biology, PhD student
RIT Alumnus 13'

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Re: Using multiple "data" directories with a single copy of JBrowse code (from July 2010 post)

Hans Vasquez-Gross
Your data is probably not organized properly.   It can't find your correct tracks.conf and trackList.json files for your individual datasets (ie chromosomes in your case).  

In my master jbrowse.conf file, the only thing I added was the [datasets] block of code at the bottom.  The only include lines you should have should be:
##sample data
include  = {dataRoot}/trackList.json
include += {dataRoot}/tracks.conf


Example dataset block of code:
[datasets.iwgsc-1AL]
url  = ?data=data/json/iwgsc-1AL
name = IWGSC-1AL

Then, in your configured iwgsc-1AL directory, you should have your individual trackList.json and tracks.conf from when you ran prepare-refseqs.pl script  (notice it is in a similar data structure).  If you have track configurations, this is where I configured the information in the tracks.conf file.  The trackList.json file should be included in the dataset configuration automatically, which will bring in the refseqs and sequencing information. In this dataset subdirectory, you should see a seq folder which will contain your data for the individual chromosome.

jbrowse havasquezgross$ ls -lah data/json/iwgsc-1AL/
total 32
drwxr-xr-x     8 havasquezgross  _www   272B Mar  3 11:53 .
drwxr-xr-x    46 havasquezgross  _www   1.5K Mar  6 10:24 ..
-rw-r--r--     1 havasquezgross  _www   535B Feb 25 11:33 .htaccess
drwxr-xr-x  4099 havasquezgross  _www   136K Feb 25 13:26 names
drwxr-xr-x  4099 havasquezgross  _www   136K Feb 20 17:35 seq
-rw-r--r--     1 havasquezgross  _www   428B Feb 25 13:25 trackList.json
-rw-r--r--     1 havasquezgross  _www   2.3K Mar  3 11:40 tracks.conf

Let me know if you're still having problems.  I may have about 10 minutes to spare for a skype call, if you would like.

Cheers,
-Hans



Hans Vasquez-Gross
Programmer
Dubcovsky and Neale Lab
Department of Plant Science
University of California at Davis
Skype: hansvg.ucd

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Re: Using multiple "data" directories with a single copy of JBrowse code (from July 2010 post)

mmacd
That seems to have fixed it! I changed the include statements and also had to make sure dataRoot = data was commented out for it to work.  
Thank you so much! 


On Fri, Mar 14, 2014 at 1:54 PM, Hans Vasquez-Gross <[hidden email]> wrote:
Your data is probably not organized properly.   It can't find your correct tracks.conf and trackList.json files for your individual datasets (ie chromosomes in your case).  

In my master jbrowse.conf file, the only thing I added was the [datasets] block of code at the bottom.  The only include lines you should have should be:
##sample data
include  = {dataRoot}/trackList.json
include += {dataRoot}/tracks.conf


Example dataset block of code:
[datasets.iwgsc-1AL]
url  = ?data=data/json/iwgsc-1AL
name = IWGSC-1AL

Then, in your configured iwgsc-1AL directory, you should have your individual trackList.json and tracks.conf from when you ran prepare-refseqs.pl script  (notice it is in a similar data structure).  If you have track configurations, this is where I configured the information in the tracks.conf file.  The trackList.json file should be included in the dataset configuration automatically, which will bring in the refseqs and sequencing information. In this dataset subdirectory, you should see a seq folder which will contain your data for the individual chromosome.

jbrowse havasquezgross$ ls -lah data/json/iwgsc-1AL/
total 32
drwxr-xr-x     8 havasquezgross  _www   272B Mar  3 11:53 .
drwxr-xr-x    46 havasquezgross  _www   1.5K Mar  6 10:24 ..
-rw-r--r--     1 havasquezgross  _www   535B Feb 25 11:33 .htaccess
drwxr-xr-x  4099 havasquezgross  _www   136K Feb 25 13:26 names
drwxr-xr-x  4099 havasquezgross  _www   136K Feb 20 17:35 seq
-rw-r--r--     1 havasquezgross  _www   428B Feb 25 13:25 trackList.json
-rw-r--r--     1 havasquezgross  _www   2.3K Mar  3 11:40 tracks.conf

Let me know if you're still having problems.  I may have about 10 minutes to spare for a skype call, if you would like.

Cheers,
-Hans



Hans Vasquez-Gross
Programmer
Dubcovsky and Neale Lab
Department of Plant Science
University of California at Davis
Skype: hansvg.ucd



--
Madolyn MacDonald
UDel Bioinformatics and Systems Biology, PhD student
RIT Alumnus 13'

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