I re-uploaded 3 BAM files using the "Upload system file paths.  runner0.log

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
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


cd /home/galaxy/galaxy-dist-9; /home/galaxy/galaxy-dist-9/set_metadata.sh
./database/files ./database/tmp . datatypes_conf.xml
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
if [ "$GALAXY_LIB" != "None" ]; then
    if [ -n "$PYTHONPATH" ]; then
        export PYTHONPATH="$GALAXY_LIB"
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
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 <n...@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
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