Runner seems to work with running the pipeline when launch from within

[htsworkflow.git] / scripts / configure_pipeline

diff --git a/scripts/configure_pipeline b/scripts/configure_pipeline
index b5126047a4e00f56d66f62abedff1097471a88c4..c70f319beeebb54baef9446e47758b1d57b41fe7 100644 (file)
--- a/scripts/configure_pipeline
+++ b/scripts/configure_pipeline
@@ -17,6 +17,8 @@ GENOME_DIR = '/data-store01/compbio/genomes/'
 
 def main(args=None):
   ci = ConfigInfo()
+  ci.analysis_dir = os.getcwd()
+  ci.base_analysis_dir, junk = os.path.split(ci.analysis_dir)
 
   #FIXME: make a better command line tool
   skip_retrieve_config = False