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annotate src/cmd_gama_headless_legacy_gen.sh @ 4:ad48b8d5acd4 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 983b35e3ac65be4a73d020fa801b906d8d750de3-dirty
author siwaa
date Mon, 09 Dec 2024 17:32:43 +0000
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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
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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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
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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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
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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13 # containing the experiment to run.
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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14 # - /path/to/outputFile.xml: path (relative or absolute) to the
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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15 # generated XML file.
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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16 #
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17 # With :
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18 # - GAMA application in folder ./software
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19 # - GAML file (containing the experiment to run) path : ./inputs/model.gaml
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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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=$1
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23 #EXPERIMENT_NAME="prey_predator"
fb186a4fb3e0 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_HEADLESS_LEGACY/galaxy-tools/gama_legacy_gen commit 14769577c04bcb2781b2d240f1f57a2342169cce-dirty
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fb186a4fb3e0 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_HEADLESS_LEGACY/galaxy-tools/gama_legacy_gen commit 14769577c04bcb2781b2d240f1f57a2342169cce-dirty
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25 HOME=$(echo $PWD)
4
ad48b8d5acd4 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_HEADLESS_LEGACY/galaxy-tools/gama_legacy_gen commit 983b35e3ac65be4a73d020fa801b906d8d750de3-dirty
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27 # !!! Passage en variables d'environnement
ad48b8d5acd4 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_HEADLESS_LEGACY/galaxy-tools/gama_legacy_gen commit 983b35e3ac65be4a73d020fa801b906d8d750de3-dirty
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28 export MY_JAVA_DIR=${HOME}/_java
ad48b8d5acd4 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_HEADLESS_LEGACY/galaxy-tools/gama_legacy_gen commit 983b35e3ac65be4a73d020fa801b906d8d750de3-dirty
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29 export MY_TEMP_DIR=${HOME}
ad48b8d5acd4 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_HEADLESS_LEGACY/galaxy-tools/gama_legacy_gen commit 983b35e3ac65be4a73d020fa801b906d8d750de3-dirty
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30
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470b8ed4ce1a planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA_HEADLESS_LEGACY/galaxy-tools/gama_legacy_gen commit f3324742c1aa0050df56ad3f868018360a10a6ab-dirty
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31 cd /opt/gama-platform/headless;
0
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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32 /bin/bash MY_gama-headless.sh -xml ${EXPERIMENT_NAME} ${HOME}/inputs/model.gaml ${HOME}/outputs/file.xml