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annotate src/cmd_gama_headless_legacy_gen.sh @ 9:382cb366533a draft

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planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_HEADLESS_LEGACY/galaxy-tools/gama_legacy_gen commit 03175a47f53f66ed4de00e6e25cf5ff4569bac5f-dirty
author siwaa
date Tue, 10 Dec 2024 10:59:08 +0000
parents 862b156b56ce
children 770e0dde4735
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fb186a4fb3e0 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_HEADLESS_LEGACY/galaxy-tools/gama_legacy_gen commit 14769577c04bcb2781b2d240f1f57a2342169cce-dirty
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1 #!/bin/bash
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3 # Headless Legacy mode.
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4 #
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5 # Command to generate a XML file corresponding to an existing experiment :
fb186a4fb3e0 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_HEADLESS_LEGACY/galaxy-tools/gama_legacy_gen commit 14769577c04bcb2781b2d240f1f57a2342169cce-dirty
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6 #. ./gama-headless.sh -xml experimentName /path/to/inputFile.gaml /path/to/outputFile.xml
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7 # with:
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8 # - -xml: flag asking the headless to generate a XML file well-formatted
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9 # for our experiment.
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10 # - experimentName: name of the experiment to run in headless.
fb186a4fb3e0 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_HEADLESS_LEGACY/galaxy-tools/gama_legacy_gen commit 14769577c04bcb2781b2d240f1f57a2342169cce-dirty
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11 # Important : experiment of 'type': 'gui'.
fb186a4fb3e0 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_HEADLESS_LEGACY/galaxy-tools/gama_legacy_gen commit 14769577c04bcb2781b2d240f1f57a2342169cce-dirty
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12 # - /path/to/inputFile.gaml: path (relative or absolute) to GAML file
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13 # containing the experiment to run.
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14 # - /path/to/outputFile.xml: path (relative or absolute) to the
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15 # generated XML file.
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16 #
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17 # With :
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18 # - GAMA application in folder ./software
fb186a4fb3e0 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_HEADLESS_LEGACY/galaxy-tools/gama_legacy_gen commit 14769577c04bcb2781b2d240f1f57a2342169cce-dirty
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19 # - GAML file (containing the experiment to run) path : ./inputs/model.gaml
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20 # - Generated XML file path : ./outputs/file.xml
fb186a4fb3e0 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_HEADLESS_LEGACY/galaxy-tools/gama_legacy_gen commit 14769577c04bcb2781b2d240f1f57a2342169cce-dirty
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22 EXPERIMENT_NAME=$1
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23 #EXPERIMENT_NAME="prey_predator"
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fb186a4fb3e0 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_HEADLESS_LEGACY/galaxy-tools/gama_legacy_gen commit 14769577c04bcb2781b2d240f1f57a2342169cce-dirty
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25 HOME=$(echo $PWD)
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27 # !!! Passage en variables d'environnement
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28 export MY_JAVA_DIR=${HOME}/_java
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29 export MY_TEMP_DIR=${HOME}/_temp_dir
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30 mkdir -p ${MY_TEMP_DIR}
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31 export MY_CONFIGURATION_DIR=${HOME}/configuration
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32 mkdir -p ${MY_CONFIGURATION_DIR}
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33 export MY_DATA_DIR=${HOME}/_data
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34 mkdir -p ${MY_DATA_DIR}
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35
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36 cd /opt/gama-platform/headless;
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37 #/bin/bash MY_gama-headless.sh -xml ${EXPERIMENT_NAME} ${HOME}/inputs/model.gaml ${HOME}/outputs/file.xml
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38 /bin/bash MY_gama-headless.sh -v -xml ${EXPERIMENT_NAME} ${HOME}/inputs/model.gaml ${HOME}/outputs/file.xml