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 > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/