Hi all,
I'm trying to configure Galaxy to talk to our SGE cluster via DRMAA. I've got jobs submitting, and can verify they are in the queue and then run via qstat (from the cluster). However, something isn't right. I'm testing with blastp using the following in universe_wsgi.ini
[galaxy:tool_runners] ncbi_blastp_wrapper = drmaa:/// ...
Job output from run.sh,
galaxy.jobs DEBUG 2012-02-02 11:49:16,707 (25) Working directory for job is: /mnt/galaxy/galaxy-central/database/job_working_directory/000/25 galaxy.jobs DEBUG 2012-02-02 11:49:16,710 dispatching job 25 to drmaa runner galaxy.jobs INFO 2012-02-02 11:49:16,818 job 25 dispatched galaxy.jobs.runners.drmaa DEBUG 2012-02-02 11:49:17,174 (25) submitting file /mnt/galaxy/galaxy-central/database/pbs/galaxy_25.sh galaxy.jobs.runners.drmaa DEBUG 2012-02-02 11:49:17,174 (25) command is: blastp -version &> /mnt/galaxy/galaxy-central/database/tmp/GALAXY_VERSION_STRING_25; python /mnt/galaxy/galaxy-central/tools/ncbi_blast_plus/hide_stderr.py blastp -query "/mnt/galaxy/galaxy-central/database/files/000/dataset_5.dat" -subject "/mnt/galaxy/galaxy-central/database/files/000/dataset_2.dat" -task blastp -evalue 0.001 -out /mnt/galaxy/galaxy-central/database/files/000/dataset_25.dat -outfmt 6 -num_threads 8 galaxy.jobs.runners.drmaa INFO 2012-02-02 11:49:17,178 (25) queued as 223 galaxy.jobs.runners.drmaa DEBUG 2012-02-02 11:49:18,175 (25/223) state change: job is queued and active galaxy.jobs.runners.drmaa DEBUG 2012-02-02 11:49:32,176 (25/223) state change: job is running galaxy.jobs.runners.drmaa DEBUG 2012-02-02 11:49:43,367 (25/223) state change: job finished normally galaxy.jobs DEBUG 2012-02-02 11:49:43,679 job 25 ended galaxy.jobs.runners.drmaa WARNING 2012-02-02 11:49:43,699 Unable to cleanup: [Errno 2] No such file or directory: '/mnt/galaxy/galaxy-central/database/job_working_directory/000/25/25.drmout' galaxy.jobs.runners.drmaa WARNING 2012-02-02 11:49:43,699 Unable to cleanup: [Errno 2] No such file or directory: '/mnt/galaxy/galaxy-central/database/job_working_directory/000/25/25.drmerr'
Interestingly, via the Galaxy interface it does seem to have captured stdout (emtpy) and stderr anyway:
<quote> Error invoking command: blastp -query /mnt/galaxy/galaxy-central/database/files/000/dataset_5.dat -subject /mnt/galaxy/galaxy-central/database/files/000/dataset_2.dat -task blastp -evalue 0.001 -out /mnt/galaxy/galaxy-central/database/files/000/dataset_25.dat -outfmt 6 -num_threads 8
[Errno 2] No such file or directory </quote>
The error in this case is some kind of path problem, which I could 'fix' by adding 'source ~/.bashrc' to the drm_template defined in lib/galaxy/jobs/runners/drmaa.py (although there should be a more elegant solution to this!).
Anyway, why is the DRMAA code giving me these warnings about missing the stdout and stderr files - even when the run runs fine?
Thanks,
Peter