Nate - Is there a specific place in the Galaxy code that forks the samtools index on bam files on the cluster or the head node?  I really need to track this down.

On Fri, Jan 13, 2012 at 12:54 PM, Ryan Golhar <ngsbioinformatics@gmail.com> wrote:
I re-uploaded 3 BAM files using the "Upload system file paths.  runner0.log shows:

galaxy.jobs DEBUG 2012-01-13 12:50:08,442 dispatching job 76 to pbs runner
galaxy.jobs INFO 2012-01-13 12:50:08,555 job 76 dispatched
galaxy.jobs.runners.pbs DEBUG 2012-01-13 12:50:08,697 (76) submitting file /home/galaxy/galaxy-dist-9/database/pbs/76.sh
galaxy.jobs.runners.pbs DEBUG 2012-01-13 12:50:08,697 (76) command is: python /home/galaxy/galaxy-dist-9/tools/data_source/upload.py /home/galaxy/galaxy-dist-9 /home/galaxy/galaxy-dist-9/datatypes_conf.xml /home/galaxy/galaxy-dist-9/database/tmp/tmpqrVYY7         208:/home/galaxy/galaxy-dist-9/database/job_working_directory/76/dataset_208_files:None         209:/home/galaxy/galaxy-dist-9/database/job_working_directory/76/dataset_209_files:None         210:/home/galaxy/galaxy-dist-9/database/job_working_directory/76/dataset_210_files:None; cd /home/galaxy/galaxy-dist-9; /home/galaxy/galaxy-dist-9/set_metadata.sh ./database/files ./database/tmp . datatypes_conf.xml ./database/job_working_directory/76/galaxy.json 
galaxy.jobs.runners.pbs DEBUG 2012-01-13 12:50:08,699 (76) queued in default queue as 114.localhost.localdomain
galaxy.jobs.runners.pbs DEBUG 2012-01-13 12:50:09,037 (76/114.localhost.localdomain) PBS job state changed from N to R
galaxy.jobs.runners.pbs DEBUG 2012-01-13 12:51:09,205 (76/114.localhost.localdomain) PBS job state changed from R to E
galaxy.jobs.runners.pbs DEBUG 2012-01-13 12:51:10,206 (76/114.localhost.localdomain) PBS job state changed from E to C
galaxy.jobs.runners.pbs DEBUG 2012-01-13 12:51:10,206 (76/114.localhost.localdomain) PBS job has completed successfully

76.sh shows:
[galaxy@bic pbs]$ more 76.sh 
#!/bin/sh
GALAXY_LIB="/home/galaxy/galaxy-dist-9/lib"
if [ "$GALAXY_LIB" != "None" ]; then
    if [ -n "$PYTHONPATH" ]; then
        export PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"
    else
        export PYTHONPATH="$GALAXY_LIB"
    fi
fi
cd /home/galaxy/galaxy-dist-9/database/job_working_directory/76
python /home/galaxy/galaxy-dist-9/tools/data_source/upload.py /home/galaxy/galaxy-dist-9 /home/galaxy/galaxy-dist-9/datatypes_conf.xml /home/galaxy
/galaxy-dist-9/database/tmp/tmpqrVYY7         208:/home/galaxy/galaxy-dist-9/database/job_working_directory/76/dataset_208_files:None         209:/
home/galaxy/galaxy-dist-9/database/job_working_directory/76/dataset_209_files:None         210:/home/galaxy/galaxy-dist-9/database/job_working_dire
ctory/76/dataset_210_files:None; cd /home/galaxy/galaxy-dist-9; /home/galaxy/galaxy-dist-9/set_metadata.sh ./database/files ./database/tmp . dataty
pes_conf.xml ./database/job_working_directory/76/galaxy.json 

Right as the job ended I check the job output files:

[galaxy@bic pbs]$ ll
total 4
-rw-rw-r-- 1 galaxy galaxy 950 Jan 13 12:50 76.sh
[galaxy@bic pbs]$ ll
total 4
-rw------- 1 galaxy galaxy   0 Jan 13 12:50 76.e
-rw------- 1 galaxy galaxy   0 Jan 13 12:50 76.o
-rw-rw-r-- 1 galaxy galaxy 950 Jan 13 12:50 76.sh

samtools is now running on the head node.


Where does Galaxy decide how to run samtools?  Maybe I can add a check of some sort to see what's going on?


On Fri, Jan 13, 2012 at 10:53 AM, Nate Coraor <nate@bx.psu.edu> wrote:
On Jan 12, 2012, at 11:41 PM, Ryan Golhar wrote:

> Any ideas as to how to fix this?  We are interested in using Galaxy to host all our NGS data.  If indexing on the head node is going to happen, then this is going to be an extremely slow process.

Could you post the contents of /home/galaxy/galaxy-dist-9/database/pbs/62.sh ?

Although I have to admit this is really baffling.  The presence of this line without an error:

   galaxy.datatypes.metadata DEBUG 2012-01-11 10:22:40,162 Cleaning up external metadata files

Indicates that metadata was set externally and the relevant metadata files were present on disk.

--nate