1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/74b6319b38b4/ changeset: 74b6319b38b4 user: natefoo date: 2012-02-06 19:16:23 summary: Bugfix for the DRMAA job name commit, ensure all characters in the job name string conform to the DRMAA spec. affected #: 1 file
diff -r e4d1dd3bdd0dfbe8562ac352d08b1f9b497d7063 -r 74b6319b38b4b3876d0b81ef1296bb5afc729cc1 lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -1,4 +1,4 @@ -import os, sys, logging, threading, time +import os, sys, logging, threading, time, string import pprint, pwd from pwd import getpwnam import subprocess @@ -168,9 +168,12 @@ # define job attributes ofile = "%s.drmout" % os.path.join(job_wrapper.working_directory, job_wrapper.get_id_tag()) efile = "%s.drmerr" % os.path.join(job_wrapper.working_directory, job_wrapper.get_id_tag()) + job_name = "g%s_%s_%s" % ( job_wrapper.job_id, job_wrapper.tool.id, job_wrapper.user ) + job_name = ''.join( map( lambda x: x if x in ( string.letters + string.digits + '_' ) else '_', job_name ) ) + jt = self.ds.createJobTemplate() jt.remoteCommand = "%s/galaxy_%s.sh" % (self.app.config.cluster_files_directory, job_wrapper.get_id_tag()) - jt.jobName = "g%s_%s_%s" % ( job_wrapper.job_id, job_wrapper.tool.id, job_wrapper.user.replace( '@', '__at__' ) ) + jt.jobName = job_name jt.outputPath = ":%s" % ofile jt.errorPath = ":%s" % efile native_spec = self.get_native_spec( runner_url )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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