On Jan 4, 2012, at 6:44 PM, Ryan Golhar wrote:

> On Wed, Jan 4, 2012 at 5:17 PM, Ryan Golhar <ngsbioinformat...@gmail.com> 
> wrote:
> I'm adding Data Libraries to my local galaxy instance.  I'm doing this by 
> importing directories that contain bam and bai files.  I see the bam/bai 
> files get added on the admin page and the Message is "This job is running".  
> qstat shows the job run and complete.  I checked my runner0.log and it 
> registers the PBS job completed successfully.  But the web page never 
> updates.  I tried to refresh the page by navigating away from it then back to 
> it, but it still reads "This job is running".  How do I fix this?
> 
> Some more information...I check my head node and I see samtools is running 
> there.  Its running 'samtools index'.  So two problems:
> 
> 1)  samtools is not using the cluster.  I assume this is a configuration 
> setting somewhere.

See set_metadata_externally in universe_wsgi.ini.  This should be set to True 
to run on the cluster.

If you haven't seen the rest of the production server documentation, see 
http://usegalaxy.org/production

> 2)  Why is galaxy trying to index the bam files if the bai files exists in 
> the same directory as the bam file.  The BAM files are sorted and have 
> 'SO:coordinate'.  I also have samtools-0.1.18 installed.

Galaxy does not yet have a method to upload BAM files with a precreated .bai.

> It also appears:
> 
> 3)  Galaxy is unable to import .bai files.   It says there was an error 
> importing these files "The uploaded binary file contains inappropriate 
> content"

See #2.  Galaxy will always create its own .bai.

> 4)  Galaxy is trying to change the permissions on the files I'm importing (as 
> links).  Thankfully the data tree is read-only.  If I'm linking Galaxy to my 
> date, why does Galaxy want to change the permissions?  This seems like 
> something it shouldn't be doing i.e. Galaxy should leave external data alone.

Hrm, this is not good.  I'll have a look at this.

--nate

> 
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