Text uploaded custom track not working

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Text uploaded custom track not working

Scott Cain
Hi All,

I've been working on this a while and haven't gotten it working, so I thought I'd ask for help from the collective wisdom.

On a GBrowse 2.54 install, I've been trying to create a simple custom track in the simple yeast data source.  The text I'm trying to upload is this:

  [wt_exons]
  glyph = segments
  wt_exon     wildtype_exons       chrI:100000..100100,100200..100300

It uploads successfully and generates a config but the track drawn doesn't contain any features in the area chrI:100,000..100,300.  The only message in the apache error log is:

Use of uninitialized value $type in string eq at /usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/Session.pm line 168

In Session.pm, I don't know why $type would be passed in undefined to the lock_flock method.  I do have session handling explicitly set to db_file in the GBrowse.conf file:

  session lock type = default  
  session driver    = driver:db_file;serializer:default
  session args      = Directory /data/var/lib/gbrowse2/sessions

Any ideas?

Thanks,
Scott

--
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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: Text uploaded custom track not working

Timothy Parnell
Hi Scott,

I see this error a lot in my instance, but without uploading a text feature file. GBrowse appears to work fine (but I have a lot of tracks and haven't tested every one), so I assumed it was mostly harmless. I admit I haven't spent a lot of time debugging it. I am using the berkeley db driver for session management.

I, too, would be grateful if someone knew what causes it.

Tim

On Sep 9, 2013, at 12:34 PM, Scott Cain <[hidden email]<mailto:[hidden email]>> wrote:

Hi All,

I've been working on this a while and haven't gotten it working, so I thought I'd ask for help from the collective wisdom.

On a GBrowse 2.54 install, I've been trying to create a simple custom track in the simple yeast data source.  The text I'm trying to upload is this:

  [wt_exons]
  glyph = segments
  wt_exon     wildtype_exons       chrI:100000..100100,100200..100300

It uploads successfully and generates a config but the track drawn doesn't contain any features in the area chrI:100,000..100,300.  The only message in the apache error log is:

Use of uninitialized value $type in string eq at /usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/Session.pm line 168

In Session.pm, I don't know why $type would be passed in undefined to the lock_flock method.  I do have session handling explicitly set to db_file in the GBrowse.conf file:

  session lock type = default
  session driver    = driver:db_file;serializer:default
  session args      = Directory /data/var/lib/gbrowse2/sessions

Any ideas?

Thanks,
Scott

--
------------------------------------------------------------------------
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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tutorial videos with LearnDevNow. Subscribe today and save!
http://pubads.g.doubleclick.net/gampad/clk?id=58041391&iu=/4140/ostg.clktrk_______________________________________________
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