Mercurial > repos > siwaa > gama_legacy_gen
changeset 11:770e0dde4735 draft default tip
planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_HEADLESS_LEGACY/galaxy-tools/gama_legacy_gen commit 8731d8cb947d6b7b65eb0fde51a4b0f44c2f4406-dirty
| author | siwaa |
|---|---|
| date | Fri, 20 Dec 2024 23:16:10 +0000 |
| parents | f57ea38d67c5 |
| children | |
| files | gama_legacy_gen.xml src/.cmd_gama_headless_legacy_gen.sh.swp src/cmd_gama_headless_legacy_gen.sh |
| diffstat | 3 files changed, 8 insertions(+), 15 deletions(-) [+] |
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--- 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 ${file_xml};
--- a/src/cmd_gama_headless_legacy_gen.sh Tue Dec 10 11:22:59 2024 +0000 +++ b/src/cmd_gama_headless_legacy_gen.sh Fri Dec 20 23:16:10 2024 +0000 @@ -23,16 +23,5 @@ #EXPERIMENT_NAME="prey_predator" HOME=$(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