[Gmod-ajax] Shared reference for multiple datasets

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

[Gmod-ajax] Shared reference for multiple datasets

Keiran Raine
Hi,

I'm having problems having multiple datasets share the same reference.  The dataset itself does't require any local data other than the reference data.

I'm having a couple of issues (probably needs a config value in the trackList.json):

1. Unless I symlink the 'seq' folder the dataset is not available.
2. Name searching is not picking up the correct configuration:

Other than this it appears to be working as expected (except for an issue with histograms which I'm trying to check I've not messed up).

Details for conf and folder structure below.

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

 The folders look like this:

cgp-jbrowse-dev[kr2]69: pwd
/data/JBrowse-1.11.0
cgp-jbrowse-dev[kr2]70: ls -l sanger/t1012/
total 12
lrwxrwxrwx 1 kr2 cancer   49 Jan  2 12:00 names -> /jbrowse/nginx/html/JBrowse/sanger/HUMAN/37/names/
lrwxrwxrwx 1 kr2 cancer    4 Jan  2 10:17 nfs -> /nfs/
lrwxrwxrwx 1 kr2 cancer   47 Jan  2 10:17 seq -> /jbrowse/nginx/html/JBrowse/sanger/HUMAN/37/seq/
-rw-r----- 1 kr2 cancer 8232 Jan  2 10:17 trackList.json
-rw-r----- 1 kr2 cancer    0 Jan  2 11:46 tracks.conf
cgp-jbrowse-dev[kr2]71: ls -l sanger/HUMAN/37/
total 168
drwxr-x---  2 kr2 cancer 102400 Jan  1 22:19 names/
drwxr-x--- 27 kr2 cancer   4096 Jan  1 22:19 seq/
-rw-r-----  1 kr2 cancer    890 Jan  1 22:19 trackList.json
drwxr-x---  3 kr2 cancer     27 Jan  1 22:19 tracks/
-rw-r-----  1 kr2 cancer      0 Jan  1 22:19 tracks.conf

The conf file for the actual dataset is attached.


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



------------------------------------------------------------------------------
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

trackList.json (8K) Download Attachment
Reply | Threaded
Open this post in threaded view
|

Re: Shared reference for multiple datasets

Robert Buels-2
You can just override a couple of things in your tracks.conf or
trackList.json files, since they are loaded after jbrowse.conf and
jbrowse_conf.json.

Something in tracks.conf like:

[general]
refSeqs = ../relative/url/of/refSeqs.json
[tracks.DNA] (or maybe [store.refseqs])
urlTemplate = ../relative/url/to/seq/{refseq_dirpath}/{refseq}-

The URLs should be relative to the conf file in which they appear.

Does that work?


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 01/02/2014 07:03 AM, Keiran Raine wrote:

> Hi,
>
> I'm having problems having multiple datasets share the same reference.
>   The dataset itself does't require any local data other than the
> reference data.
>
> I'm having a couple of issues (probably needs a config value in the
> trackList.json):
>
> 1. Unless I symlink the 'seq' folder the dataset is not available.
> 2. Name searching is not picking up the correct configuration:
> http://cgp-jbrowse-dev.internal.sanger.ac.uk:8000/JBrowse/sanger/t1012/names/root.json
> 404(Not found)
>
> Other than this it appears to be working as expected (except for an
> issue with histograms which I'm trying to check I've not messed up).
>
> Details for conf and folder structure below.
>
> Keiran Raine
> Principal Bioinformatician
> Cancer Genome Project
> Wellcome Trust Sanger Institute
>
> [hidden email] <mailto:[hidden email]>
> Tel:+44 (0)1223 834244 Ext: 7703
> Office: H104
>
>   The folders look like this:
>
> cgp-jbrowse-dev[kr2]69: pwd
> /data/JBrowse-1.11.0
> cgp-jbrowse-dev[kr2]70: ls -l sanger/t1012/
> total 12
> lrwxrwxrwx 1 kr2 cancer   49 Jan  2 12:00 names ->
> /jbrowse/nginx/html/JBrowse/sanger/HUMAN/37/names/
> lrwxrwxrwx 1 kr2 cancer    4 Jan  2 10:17 nfs -> /nfs/
> lrwxrwxrwx 1 kr2 cancer   47 Jan  2 10:17 seq ->
> /jbrowse/nginx/html/JBrowse/sanger/HUMAN/37/seq/
> -rw-r----- 1 kr2 cancer 8232 Jan  2 10:17 trackList.json
> -rw-r----- 1 kr2 cancer    0 Jan  2 11:46 tracks.conf
> cgp-jbrowse-dev[kr2]71: ls -l sanger/HUMAN/37/
> total 168
> drwxr-x---  2 kr2 cancer 102400 Jan  1 22:19 names/
> drwxr-x--- 27 kr2 cancer   4096 Jan  1 22:19 seq/
> -rw-r-----  1 kr2 cancer    890 Jan  1 22:19 trackList.json
> drwxr-x---  3 kr2 cancer     27 Jan  1 22:19 tracks/
> -rw-r-----  1 kr2 cancer      0 Jan  1 22:19 tracks.conf
>
> The conf file for the actual dataset is attached.
>
>
> -- The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a
> company registered in England with number 2742969, whose registered
> office is 215 Euston Road, London, NW1 2BE.
>
>
>
>
>
> ------------------------------------------------------------------------------
> Rapidly troubleshoot problems before they affect your business. Most IT
> organizations don't have a clear picture of how application performance
> affects their revenue. With AppDynamics, you get 100% visibility into your
> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
> http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

------------------------------------------------------------------------------
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
Reply | Threaded
Open this post in threaded view
|

Re: Shared reference for multiple datasets

Keiran Raine
Hi Robert,

I've added the refSeqs entry (in trackList.json) and also the 'names' section to get searching working.

Config as follows (removed non reference tracks at '…' for brevity):

{
"refSeqs" : "../HUMAN/37/seq/refSeqs.json", "names" : { "url" : "../HUMAN/37/names", "type" : "Hash" },
   "tracks" : [
      {
         "showTranslation" : "false",
         "key" : "DNA",
         "chunkSize" : 20000,
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "urlTemplate" : "../HUMAN/37/seq/{refseq_dirpath}/{refseq}-",
         "compress" : 1,
         "category" : "Reference",
         "type" : "SequenceTrack",
         "label" : "dna"
      },
      {
         "displayMode" : "compact",
         "style" : {
            "className" : "feature"
         },
         "key" : "Protein Coding Genes",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "trackType" : "JBrowse/View/Track/CanvasFeatures",
         "urlTemplate" : "../HUMAN/37/tracks/protein_coding/{refseq}/trackData.jsonz",
         "compress" : 1,
         "category" : "Reference",
         "type" : "JBrowse/View/Track/CanvasFeatures",
         "label" : "protein_coding"
      },
      ...
   ],
   "dataset_id" : "t1012",
   "formatVersion" : 1
}

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

On 3 Jan 2014, at 07:15, Robert Buels <[hidden email]> wrote:

You can just override a couple of things in your tracks.conf or trackList.json files, since they are loaded after jbrowse.conf and jbrowse_conf.json.

Something in tracks.conf like:

[general]
refSeqs = ../relative/url/of/refSeqs.json
[tracks.DNA] (or maybe [store.refseqs])
urlTemplate = ../relative/url/to/seq/{refseq_dirpath}/{refseq}-

The URLs should be relative to the conf file in which they appear.

Does that work?


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 01/02/2014 07:03 AM, Keiran Raine wrote:
Hi,

I'm having problems having multiple datasets share the same reference.
 The dataset itself does't require any local data other than the
reference data.

I'm having a couple of issues (probably needs a config value in the
trackList.json):

1. Unless I symlink the 'seq' folder the dataset is not available.
2. Name searching is not picking up the correct configuration:
http://cgp-jbrowse-dev.internal.sanger.ac.uk:8000/JBrowse/sanger/t1012/names/root.json
404(Not found)

Other than this it appears to be working as expected (except for an
issue with histograms which I'm trying to check I've not messed up).

Details for conf and folder structure below.

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

[hidden email] <mailto:[hidden email]>
Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

 The folders look like this:

cgp-jbrowse-dev[kr2]69: pwd
/data/JBrowse-1.11.0
cgp-jbrowse-dev[kr2]70: ls -l sanger/t1012/
total 12
lrwxrwxrwx 1 kr2 cancer   49 Jan  2 12:00 names ->
/jbrowse/nginx/html/JBrowse/sanger/HUMAN/37/names/
lrwxrwxrwx 1 kr2 cancer    4 Jan  2 10:17 nfs -> /nfs/
lrwxrwxrwx 1 kr2 cancer   47 Jan  2 10:17 seq ->
/jbrowse/nginx/html/JBrowse/sanger/HUMAN/37/seq/
-rw-r----- 1 kr2 cancer 8232 Jan  2 10:17 trackList.json
-rw-r----- 1 kr2 cancer    0 Jan  2 11:46 tracks.conf
cgp-jbrowse-dev[kr2]71: ls -l sanger/HUMAN/37/
total 168
drwxr-x---  2 kr2 cancer 102400 Jan  1 22:19 names/
drwxr-x--- 27 kr2 cancer   4096 Jan  1 22:19 seq/
-rw-r-----  1 kr2 cancer    890 Jan  1 22:19 trackList.json
drwxr-x---  3 kr2 cancer     27 Jan  1 22:19 tracks/
-rw-r-----  1 kr2 cancer      0 Jan  1 22:19 tracks.conf

The conf file for the actual dataset is attached.


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





------------------------------------------------------------------------------
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk



_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax



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

------------------------------------------------------------------------------
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax