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809804e
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Figure out the absolute path to the runfolder for passing to the post_run
author
Diane Trout
<diane@caltech.edu>
Sat, 17 Oct 2009 00:27:36 +0000
(
00:27
+0000)
committer
Diane Trout
<diane@caltech.edu>
Sat, 17 Oct 2009 00:27:36 +0000
(
00:27
+0000)
command
htsworkflow/pipelines/retrieve_config.py
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diff --git
a/htsworkflow/pipelines/retrieve_config.py
b/htsworkflow/pipelines/retrieve_config.py
index 136bb5a50c60ff8890a35b6b579426ca6f593257..dd60f6090188ab59260242de9c2a5b69014d1eae 100644
(file)
--- a/
htsworkflow/pipelines/retrieve_config.py
+++ b/
htsworkflow/pipelines/retrieve_config.py
@@
-149,7
+149,8
@@
def format_gerald_config(options, flowcell_info, genome_map):
# add in option for running script after
if options.post_run is not None:
# add in option for running script after
if options.post_run is not None:
- post_run = options.post_run % {'runfolder': options.runfolder}
+ runfolder = os.path.abspath(options.runfolder)
+ post_run = options.post_run % {'runfolder': runfolder}
config += ['POST_RUN_COMMAND %s' % (post_run,) ]
config += [''] # force trailing newline
config += ['POST_RUN_COMMAND %s' % (post_run,) ]
config += [''] # force trailing newline
@@
-203,8
+204,9
@@
Config File:
Example Config File:
[%s]
Example Config File:
[%s]
- config_host=http://somewhere.domain:port
- genome_dir=/path to search for genomes
+ config_host: http://somewhere.domain:port
+ genome_dir: /path to search for genomes
+ post_run: runfolder -o <destdir> %%(runfolder)s
""" % (CONFIG_SYSTEM, CONFIG_USER, GERALD_CONFIG_SECTION)
""" % (CONFIG_SYSTEM, CONFIG_USER, GERALD_CONFIG_SECTION)