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Passing GALAXY_DATA_INDEX_DIR on to pbs environment.

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Nate Coraor
2008-03-21 18:50:35 +00:00
parent cd52cabd48
commit 38b7f6bd5e
1 changed files with 4 additions and 2 deletions
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lib/galaxy/jobs/runners/pbs.py
+4 -2
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@@ -21,6 +21,7 @@ pbs_template = """#!/bin/sh
export LC_ALL='%s'
export PATH='%s'
export PYTHONPATH='%s'
export GALAXY_DATA_INDEX_DIR='%s'
cd %s
%s
"""
@@ -29,6 +30,7 @@ pbs_symlink_template = """#!/bin/sh
export LC_ALL='%s'
export PATH='%s'
export PYTHONPATH='%s'
export GALAXY_DATA_INDEX_DIR='%s'
for dataset in %s; do
dir=`dirname $dataset`
file=`basename $dataset`
@@ -152,9 +154,9 @@ class PBSJobRunner( object ):
# write the job script
if self.app.config.pbs_stage_path != '':
script = pbs_symlink_template % (os.environ['LC_ALL'], os.environ['NODEPATH'], os.environ['PYTHONPATH'], " ".join(job_wrapper.get_input_fnames() + job_wrapper.get_output_fnames()), self.app.config.pbs_stage_path, exec_dir, command_line)
script = pbs_symlink_template % (os.environ['LC_ALL'], os.environ['NODEPATH'], os.environ['PYTHONPATH'], os.environ['GALAXY_DATA_INDEX_DIR'], " ".join(job_wrapper.get_input_fnames() + job_wrapper.get_output_fnames()), self.app.config.pbs_stage_path, exec_dir, command_line)
else:
script = pbs_template % (os.environ['LC_ALL'], os.environ['NODEPATH'], os.environ['PYTHONPATH'], exec_dir, command_line)
script = pbs_template % (os.environ['LC_ALL'], os.environ['NODEPATH'], os.environ['PYTHONPATH'], os.environ['GALAXY_DATA_INDEX_DIR'], exec_dir, command_line)
job_file = "%s/database/pbs/%s.sh" % (os.getcwd(), job_wrapper.job_id)
fh = file(job_file, "w")
fh.write(script)