From 8930d66403a9bf20b3860da0a2aa93f7874e15d7 Mon Sep 17 00:00:00 2001 From: RoanKanninga Date: Thu, 20 Jul 2017 10:39:05 +0200 Subject: [PATCH] fix test (part 6) --- test/test_pipeline.sh | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/test/test_pipeline.sh b/test/test_pipeline.sh index a39b0a28..2eaebacc 100644 --- a/test/test_pipeline.sh +++ b/test/test_pipeline.sh @@ -56,7 +56,9 @@ cp generate_template.sh ${workfolder}/generatedscripts/PlatinumSubset/generate_t ## Grep used version of molgenis compute out of the parameters file fgrep "computeVersion," parameters.csv > ${workfolder}/generatedscripts/PlatinumSubset/mcVersion.txt -perl -pi -e 's|module load NGS_DNA/3.4.1|EBROOTNGS_DNA=/groups/umcg-gaf/tmp04/tmp/NGS_DNA/|' ${workfolder}/generatedscripts/PlatinumSubset/generate_template.sh +NGS_DNA_VERSION=NGS_DNA/3.4.1 +module load $NGS_DNA_VERSION +perl -pi -e "s|module load $NGS_DNA_VERSION|EBROOTNGS_DNA=/groups/umcg-gaf/tmp04/tmp/NGS_DNA/|" ${workfolder}/generatedscripts/PlatinumSubset/generate_template.sh perl -pi -e 's|PROJECT=projectXX|PROJECT=PlatinumSubset|' ${workfolder}/generatedscripts/PlatinumSubset/generate_template.sh perl -pi -e 's|RUNID=runXX|RUNID=run01|' ${workfolder}/generatedscripts/PlatinumSubset/generate_template.sh perl -pi -e 's|ngsversion=.*|ngsversion="test";\\|' ${workfolder}/generatedscripts/PlatinumSubset/generate_template.sh @@ -71,7 +73,7 @@ cd ${workfolder}/generatedscripts/PlatinumSubset/ sh generate_template.sh cd scripts -perl -pi -e 's|module load \$ngsversion|EBROOTNGS_DNA=/groups/umcg-gaf/tmp04/tmp/NGS_DNA/\n#string computeVersion\nmodule load Molgenis-Compute/\${computeVersion}|' *.sh +perl -pi -e 's|module load \$ngsversion|EBROOTNGS_DNA=/groups/umcg-gaf/tmp04/tmp/NGS_DNA/\n|' *.sh sh submit.sh cd ${workfolder}/projects/PlatinumSubset/run01/jobs/