Mercurial > repos > patrick_chabrier > carboseq_s

changeset 3:40f76111ab6c draft

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Uploaded
author siwaa
date Tue, 25 Jun 2024 14:58:11 +0000
parents bf6c51b72a10
children b5a6c2d3e5e7
files carboseqSimulator.xml
diffstat 1 files changed, 2 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/carboseqSimulator.xml	Tue Jun 25 14:02:45 2024 +0000
+++ b/carboseqSimulator.xml	Tue Jun 25 14:58:11 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.2">
+<tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.3">
   <description>To run the CarboSeq simulator</description>
   <requirements>
     <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:develop-695457e0</container>
@@ -9,7 +9,7 @@
   unzip -d input ${input} &&
   set -a ;source /usr/local/src/myscripts/.env &&
   mkdir tmp &&
-  export TMP=$(pwd)/tmp &&
+  export TMP=\$(realpath -s 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}"
     ]]>