1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/73e2dd2c815b/ changeset: 73e2dd2c815b user: natefoo date: 2012-02-06 18:39:19 summary: A couple of job running path resolution changes, fixes #713 (thanks Peter) affected #: 2 files
diff -r e38a9eb21336ce56ba6c5ec53e7492853c2c4088 -r 73e2dd2c815bf289751951d6127be2a14d7163e6 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -577,8 +577,8 @@ job_tool = self.app.toolbox.tools_by_id.get( job.tool_id, None ) def in_directory( file, directory ): # Make both absolute. - directory = os.path.realpath( directory ) - file = os.path.realpath( file ) + directory = os.path.abspath( directory ) + file = os.path.abspath( file )
#Return true, if the common prefix of both is equal to directory #e.g. /a/b/c/d.rst and directory is /a/b, the common prefix is /a/b
diff -r e38a9eb21336ce56ba6c5ec53e7492853c2c4088 -r 73e2dd2c815bf289751951d6127be2a14d7163e6 lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -166,8 +166,8 @@ job_wrapper.change_state( model.Job.states.QUEUED )
# define job attributes - ofile = "%s.drmout" % os.path.join(os.getcwd(), job_wrapper.working_directory, job_wrapper.get_id_tag()) - efile = "%s.drmerr" % os.path.join(os.getcwd(), job_wrapper.working_directory, job_wrapper.get_id_tag()) + 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()) jt = self.ds.createJobTemplate() jt.remoteCommand = "%s/galaxy_%s.sh" % (self.app.config.cluster_files_directory, job_wrapper.get_id_tag()) jt.outputPath = ":%s" % ofile
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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