removing unnecessary checkEnvironment script (logic is now inside gen…

…erate_template
molgenis · Aug 16, 2016 · 3ee46b4 · 3ee46b4
1 parent ba0ae4a
commit 3ee46b4
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Showing 6 changed files with 16 additions and 51 deletions.
diff --git a/checkEnvironment.sh b/checkEnvironment.sh
diff --git a/generate_template.sh b/generate_template.sh
@@ -3,12 +3,11 @@
 module load NGS_DNA/3.2.4
 module list 
 HOST=$(hostname)
-##Running script for checking the environment variables
-sh ${EBROOTNGS_DNA}/checkEnvironment.sh ${HOST}
+thisDir=$(pwd)
 
-ENVIRONMENT_PARAMETERS=$(awk '{print $1}' ./environment_checks.txt)
-TMPDIR=$(awk '{print $2}' ./environment_checks.txt)
-GROUP=$(awk '{print $3}' ./environment_checks.txt)
+ENVIRONMENT_PARAMETERS="parameters_${HOST%%.*}.csv"
+TMPDIR=$(cd ../../ && ${thisDir} )
+GROUP=$(cd ../../../ && ${thisDir} )
 
 PROJECT=projectXX
 WORKDIR="/groups/${GROUP}/${TMPDIR}"
@@ -38,6 +37,11 @@ then
     	rm -rf ${WORKDIR}/generatedscripts/${PROJECT}/out.csv
 fi
 
+echo "tmpName,${TMPDIR}" > ${WORKDIR}/generatedscripts/${PROJECT}/tmpdir_parameters.csv 
+
+perl ${EBROOTNGS_DNA}/convertParametersGitToMolgenis.pl ${WORKDIR}/generatedscripts/${PROJECT}/tmpdir_parameters.csv > \
+${WORKDIR}/generatedscripts/${PROJECT}/tmpdir_parameters_converted.csv
+
 perl ${EBROOTNGS_DNA}/convertParametersGitToMolgenis.pl ${EBROOTNGS_DNA}/parameters.csv > \
 ${WORKDIR}/generatedscripts/${PROJECT}/out.csv
 
@@ -51,6 +55,7 @@ sh $EBROOTMOLGENISMINCOMPUTE/molgenis_compute.sh \
 -p ${WORKDIR}/generatedscripts/${PROJECT}/out.csv \
 -p ${WORKDIR}/generatedscripts/${PROJECT}/environment_parameters.csv \
 -p ${WORKDIR}/generatedscripts/${PROJECT}/group_parameters.csv \
+-p ${WORKDIR}/generatedscripts/${PROJECT}/tmpdir_parameters_converted.csv \
 -p ${EBROOTNGS_DNA}/batchIDList${BATCH}.csv \
 -p ${WORKDIR}/generatedscripts/${PROJECT}/${PROJECT}.csv \
 -w ${EBROOTNGS_DNA}/create_in-house_ngs_projects_workflow.csv \
@@ -62,6 +67,7 @@ group_parameters=${WORKDIR}/generatedscripts/${PROJECT}/group_parameters.csv;\
 groupname=${GROUP};\
 ngsversion=$(module list | grep -o -P 'NGS_DNA(.+)');\
 environment_parameters=${WORKDIR}/generatedscripts/${PROJECT}/environment_parameters.csv;\
+tmpdir_parameters=${WORKDIR}/generatedscripts/${PROJECT}/tmpdir_parameters_converted.csv;\
 batchIDList=${EBROOTNGS_DNA}/batchIDList${BATCH}.csv;\
 worksheet=${WORKDIR}/generatedscripts/${PROJECT}/${PROJECT}.csv" \
 -weave \

diff --git a/parameters_calculon.csv b/parameters_calculon.csv
@@ -1,5 +1,4 @@
 queue,ll
-tmpName,tmp04
 prmName,prm02
 root,/
 appsDir,${root}/apps/

diff --git a/parameters_leela.csv b/parameters_leela.csv
@@ -0,0 +1,5 @@
+queue,ll
+prmName,prm02
+root,/
+appsDir,${root}/apps/
+toolChain,goolf-1.7.20
diff --git a/parameters_leucine-zipper.csv b/parameters_leucine-zipper.csv
@@ -1,5 +1,4 @@
 queue,lz-compute
-tmpName,tmp06
 prmName,prm02
 root,/
 appsDir,${root}/apps/

diff --git a/parameters_zinc-finger.csv b/parameters_zinc-finger.csv
@@ -1,5 +1,4 @@
 queue,ll
-tmpName,tmp05
 prmName,prm02
 root,/
 appsDir,${root}/apps/