From f8e6277627aa511b72ecfcc8e8a4545b1c5b51bf Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Sat, 17 Oct 2009 00:27:36 +0000 Subject: [PATCH] Figure out the absolute path to the runfolder for passing to the post_run command --- htsworkflow/pipelines/retrieve_config.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/htsworkflow/pipelines/retrieve_config.py b/htsworkflow/pipelines/retrieve_config.py index 136bb5a..dd60f60 100644 --- 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: - 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 @@ -203,8 +204,9 @@ Config File: 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 %%(runfolder)s """ % (CONFIG_SYSTEM, CONFIG_USER, GERALD_CONFIG_SECTION) -- 2.30.2