Mercurial > repos > patrick_chabrier > carboseq_s

changeset 5:4c1a7c22e770 draft

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Uploaded
author siwaa
date Wed, 26 Jun 2024 06:43:43 +0000
parents b5a6c2d3e5e7
children 29b8cd5389bf
files carboseqSimulator.xml
diffstat 1 files changed, 3 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/carboseqSimulator.xml	Tue Jun 25 15:44:17 2024 +0000
+++ b/carboseqSimulator.xml	Wed Jun 26 06:43:43 2024 +0000
@@ -1,17 +1,13 @@
-<tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.3">
+<tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.4">
   <description>To run the CarboSeq simulator</description>
   <requirements>
     <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:develop-695457e0</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[
-  bash -e -c "mkdir inputs &&
-  mkdir output &&
+  bash -e -c "mkdir output &&
   unzip -d input ${input} &&
-  set -a ;source /usr/local/src/myscripts/.env &&
   mkdir tmp &&
-  export TMP=\$(realpath -s tmp) &&
-  pwd &&
-  ls &&
+  export TMPDIR="\${PWD}/tmp" &&
   Rscript /usr/local/src/myscripts/scenarios/run-sim-perf/run.r --url=https://coby.infosol.inrae.fr:7777/semantify --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --NBCores=\${GALAXY_SLOTS:-4}&&
   mv output/* ${output}"
     ]]>