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changeset 13:9ad79c2d8e0b draft

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"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/75b22cbc75bbd0c301eabef3a734ca47468bb47e/toos/CarboSeqSimulator commit 75b22cbc75bbd0c301eabef3a734ca47468bb47e-dirty"
author siwaa
date Thu, 19 Sep 2024 17:57:10 +0000
parents 7e43dc776bda
children e455667fe22f
files carboseqSimulator.xml
diffstat 1 files changed, 4 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/carboseqSimulator.xml	Thu Sep 19 15:58:11 2024 +0000
+++ b/carboseqSimulator.xml	Thu Sep 19 17:57:10 2024 +0000
@@ -1,15 +1,15 @@
 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.16">
   <description>To run the CarboSeq simulator</description>
-  <environment_variables>
-    <environment_variable name="TMPDIR">\$(realpath -s tmp)</environment_variable>
-  </environment_variables>
   <requirements>
     <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:main</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[
   (env | grep DOCKER_IMAGE) &&
   printf " Image  Reg   : \$s\n" \$(env | grep DOCKER_IMAGE) &&
-  bash -e -c "mkdir tmp &&
+  export "TMPDIR=\$(realpath -s tmp)" &&
+  bash -e -c "
+  echo \$TMPDIR &&
+  mkdir tmp &&
   mkdir output &&
   unzip -d input ${input} &&
   cp /usr/local/src/myscripts/semantifier.jar . &&