[Gmod-ajax] Setup JBrowse question

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[Gmod-ajax] Setup JBrowse question

zhilianghu
I did a fresh setup of JBrowse, and Volvox test data seems working:
  http://i.animalgenome.org/jbrowse/

As my first test case I try to follow the quick start:
  > setup.sh

then set a reference bovine chromosome 1:

  > bin/flatfile-to-json.pl --gbk /path/to/chr1.gbk \
                            --out data/cattle
                            --key "BTAU.chr1"
                            --tracklabel "BTAU.chr1"

and this quickly created 2 very small files:

  -rw-r--r-- 1 123 456  411 Jul  5 21:09 trackList.json
  -rw-r--r-- 1 123 456    0 Jul  5 21:00 tracks.conf

File "trackList.json":
{
    "tracks" : [
       {
          "style" : {
             "className" : "feature"
          },
          "key" : "BTAU.chr1",
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "trackType" : null,
          "urlTemplate" : "tracks/BTAU.chr1/{refseq}/trackData.json",
          "compress" : 0,
          "type" : "FeatureTrack",
          "label" : "BTAU.chr1"
       }
    ],
    "formatVersion" : 1
}

at this point I am kind of lost as what to follow exactly in order to
view the track. The online wiki seems to me a big jump for me
http://gmod.org/wiki/JBrowse_Tutorial  Any step by step procedure or
sample to folow will be appreciated.

Thanks in advance.

Zhiliang

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Re: Setup JBrowse question

Colin
If you haven't already, you also have to run prepare-refseqs.pl

-Colin


On Tue, Jul 8, 2014 at 8:27 PM, Zhiliang Hu <[hidden email]> wrote:
I did a fresh setup of JBrowse, and Volvox test data seems working:
  http://i.animalgenome.org/jbrowse/

As my first test case I try to follow the quick start:
  > setup.sh

then set a reference bovine chromosome 1:

  > bin/flatfile-to-json.pl --gbk /path/to/chr1.gbk \
                            --out data/cattle
                            --key "BTAU.chr1"
                            --tracklabel "BTAU.chr1"

and this quickly created 2 very small files:

  -rw-r--r-- 1 123 456  411 Jul  5 21:09 trackList.json
  -rw-r--r-- 1 123 456    0 Jul  5 21:00 tracks.conf

File "trackList.json":
{
    "tracks" : [
       {
          "style" : {
             "className" : "feature"
          },
          "key" : "BTAU.chr1",
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "trackType" : null,
          "urlTemplate" : "tracks/BTAU.chr1/{refseq}/trackData.json",
          "compress" : 0,
          "type" : "FeatureTrack",
          "label" : "BTAU.chr1"
       }
    ],
    "formatVersion" : 1
}

at this point I am kind of lost as what to follow exactly in order to
view the track. The online wiki seems to me a big jump for me
http://gmod.org/wiki/JBrowse_Tutorial  Any step by step procedure or
sample to folow will be appreciated.

Thanks in advance.

Zhiliang

------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax


------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
Gmod-ajax mailing list
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https://lists.sourceforge.net/lists/listinfo/gmod-ajax