# HG changeset patch
# User siwaa
# Date 1734736570 0
# Node ID 770e0dde4735cf27a4c8542aadbd51147bb42ccc
# Parent  f57ea38d67c5fdaeef4c81122d1059be5c6b9ef0
planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_HEADLESS_LEGACY/galaxy-tools/gama_legacy_gen commit 8731d8cb947d6b7b65eb0fde51a4b0f44c2f4406-dirty

diff -r f57ea38d67c5 -r 770e0dde4735 gama_legacy_gen.xml
--- a/gama_legacy_gen.xml	Tue Dec 10 11:22:59 2024 +0000
+++ b/gama_legacy_gen.xml	Fri Dec 20 23:16:10 2024 +0000
@@ -5,7 +5,7 @@
   <requirements>
 
     <!-- singularity --> 
-    <container type="singularity">oras://registry.forgemia.inra.fr/nathalie.rousse/use/gama_headless:74ad70560393b1198b7f329fa4f1355643cc2250</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/nathalie.rousse/use/gama_headless:0356ba7eb250433405698597a802d8a6b4e04967</container>
 
     <!-- image locale
     <container type="singularity">/home/nrousse/workspace_git/SIWAA_regroup/USE_branch_gama/use/GAMA_HEADLESS_LEGACY/containers/gama_headless.simg</container -->
@@ -13,9 +13,13 @@
 
   <command detect_errors="aggressive">
     <![CDATA[
-    mkdir -p inputs; mkdir -p outputs;
+    mkdir -p software; mkdir -p inputs; mkdir -p outputs;
+    cp $__tool_directory__/src/MY_gama-headless.sh .;
     cp $__tool_directory__/src/cmd_gama_headless_legacy_gen.sh .;
     cp ${model_gaml} inputs/model.gaml;
+    cp -fr /opt/gama-platform software/.;
+    cp MY_gama-headless.sh software/gama-platform/headless/. ;
+    chmod -R 777 software;
     /bin/bash cmd_gama_headless_legacy_gen.sh ${experiment_name} > outputs/GEN.txt;
     xmlstarlet edit --inplace --update "//Simulation/@sourcePath" --value "model.gaml" outputs/file.xml;
     cp outputs/file.xml ${file_xml};
diff -r f57ea38d67c5 -r 770e0dde4735 src/.cmd_gama_headless_legacy_gen.sh.swp
Binary file src/.cmd_gama_headless_legacy_gen.sh.swp has changed
diff -r f57ea38d67c5 -r 770e0dde4735 src/cmd_gama_headless_legacy_gen.sh
--- a/src/cmd_gama_headless_legacy_gen.sh	Tue Dec 10 11:22:59 2024 +0000
+++ b/src/cmd_gama_headless_legacy_gen.sh	Fri Dec 20 23:16:10 2024 +0000
@@ -23,16 +23,5 @@
 #EXPERIMENT_NAME="prey_predator"
 
 HOME=$(echo $PWD)
-
-# !!! Passage en variables d'environnement
-export MY_JAVA_DIR=${HOME}/_java
-export MY_TEMP_DIR=${HOME}/_temp_dir
-mkdir -p ${MY_TEMP_DIR}
-export MY_CONFIGURATION_DIR=${HOME}/configuration
-mkdir -p ${MY_CONFIGURATION_DIR}
-export MY_DATA_DIR=${HOME}/_data
-mkdir -p ${MY_DATA_DIR}
-
-cd /opt/gama-platform/headless;
-#/bin/bash MY_gama-headless.sh -xml ${EXPERIMENT_NAME} ${HOME}/inputs/model.gaml ${HOME}/outputs/file.xml
-/bin/bash MY_gama-headless.sh -v -xml ${EXPERIMENT_NAME} ${HOME}/inputs/model.gaml ${HOME}/outputs/file.xml
+cd software/gama-platform/headless;
+/bin/bash MY_gama-headless.sh -xml ${EXPERIMENT_NAME} ${HOME}/inputs/model.gaml ${HOME}/outputs/file.xml