From 004bbae6c7ddfb8c952270781974591407502279 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Wed, 2 Jul 2014 16:35:35 -0400 Subject: [PATCH] refer template directly --- crunch_scripts/arvados-bcbio-nextgen.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/crunch_scripts/arvados-bcbio-nextgen.py b/crunch_scripts/arvados-bcbio-nextgen.py index 070e8cdbaf..692ace3df8 100755 --- a/crunch_scripts/arvados-bcbio-nextgen.py +++ b/crunch_scripts/arvados-bcbio-nextgen.py @@ -54,9 +54,7 @@ with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/tool_data_table_conf. ''') -os.mkdir("/usr/local/share/bcbio-nextgen/galaxy/templates") - -with open("/usr/local/share/bcbio-nextgen/galaxy/templates/gatk-variant.yaml", "w") as f: +with open("/tmp/crunch-job/gatk-variant.yaml", "w") as f: f.write(''' # Template for whole genome Illumina variant calling with GATK pipeline --- @@ -96,7 +94,7 @@ with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/sam_fa_indices.loc", os.chdir(arvados.current_task().tmpdir) -rcode = subprocess.call(["bcbio_nextgen.py", "--workflow", "template", "gatk-variant", "project1", +rcode = subprocess.call(["bcbio_nextgen.py", "--workflow", "template", "/tmp/crunch-job/gatk-variant.yaml", "project1", subst.do_substitution(p, "$(R1)"), subst.do_substitution(p, "$(R2)")]) -- 2.30.2