On Wed, Jan 4, 2012 at 5:17 PM, Ryan Golhar <ngsbioinformatics@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.

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.