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changeset 12:614bed83ba5d draft

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planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA/galaxy-tools commit 927c1d94ea613d36a1b4b8d048ba21ad43a6f55e-dirty
author siwaa
date Mon, 10 Jun 2024 08:44:00 +0000
parents 8623205348e5
children 13296d4a29cf
files :q ESSAISENCOURS.txt gama_tool.xml src/:wq
diffstat 4 files changed, 14 insertions(+), 184 deletions(-) [+]
line wrap: on
line diff
--- a/:q	Fri Jun 07 17:37:53 2024 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,88 +0,0 @@
-<tool id="gama_tool" name="gama" version="1.0.0f">
-
-  <description>tool for GAMA Platform</description>
-
-  <requirements>
-
-    <!-- singularity -->
-    <container type="singularity">oras://registry.forgemia.inra.fr/nathalie.rousse/use/gama:d01c3645810b3e5bf1b21170fd24d21fe1f831ec</container>
-
-    <!-- image locale 
-    <container type="singularity">/home/nrousse/workspace_git/SIWAA_regroup/USE_branch_gama/use/GAMA/containers/gama.simg</container -->
-  </requirements>
-
-  <command detect_errors="aggressive">
-    <![CDATA[
-    cp -fr /opt/gama-platform .;
-    cp $__tool_directory__/src/MY_predatorPrey.gaml gama-platform/headless/samples/predatorPrey/.;
-    cp $__tool_directory__/src/MY_gama-headless.sh gama-platform/headless/.;
-    cp $__tool_directory__/src/MY_sequential_example.py .;
-    cp $__tool_directory__/src/cmd_gama_headless.sh .;
-    cp $__tool_directory__/src/cmd_python_client.sh .;
-    /bin/bash cmd_gama_headless.sh > run_server.txt & date > TTT.txt && sleep 120 && echo "fin sleep" >> TTT.txt && date >> TTT.txt && /bin/bash cmd_python_client.sh $nb_preys_init $nb_predators_init $nb_more_steps > run_client.txt;
-    cp run_server.txt ${run_server_txt};
-    cp run_client.txt ${run_client_txt};
-    cp gama-platform/headless/samples/predatorPrey/results.txt ${results_txt};
-    ]]>
-  </command>
-
-  <inputs>
-
-    <param name="nb_preys_init" optional="true" type="integer"
-           value="200" min="0" max="1000"
-           label="nb_preys_init" help="[0, 1000]" />
-
-    <param name="nb_predators_init" optional="true" type="integer"
-           value="20" min="0" max="200"
-           label="nb_predators_init" help="[0, 200]" />
-
-    <param name="nb_more_steps" optional="true" type="integer"
-           value="10" min="4" max="100"
-           label="nb_more_steps" help="[4,100]" />
-
-  </inputs>
-
-  <outputs>
-    <data format="txt" name="run_server_txt" label="run_server_txt"/>
-    <data format="txt" name="run_client_txt" label="run_client_txt"/>
-    <data format="txt" name="results_txt" label="results_txt"/>
-  </outputs>
-
-  <tests>
-  </tests>
-
-  <help><![CDATA[
-
-Desc:
-
------
-
-gama_tool.xml tool running a GAMA Python client interacting with gama-server
-(Headless server) concerning a "Predator Prey" agent-based simulator.
-
-Code: MY_sequential_example.py
-
-Inputs:
-
-  - nb_preys_init
-  - nb_predators_init
-  - nb_more_steps
-
-Outputs:
-
-  - results_txt file (.txt) : produced while running the simulator
-    (cf 'reflex save_result' into MY_predatorPrey.gaml).
-  - run_server_txt file (.txt) : gama-server screen display capture
-  - run_client_txt file (.txt) : gama-client screen display capture
-
-Credits:
-
---------
-
--  Author: Nathalie Rousse nathalie.rousse@inrae.fr
--  Copyright: INRAE
-
-  ]]>
-  </help>
-
-</tool>
--- a/ESSAISENCOURS.txt	Fri Jun 07 17:37:53 2024 +0000
+++ b/ESSAISENCOURS.txt	Mon Jun 10 08:44:00 2024 +0000
@@ -1,20 +1,26 @@
 #------------------------------------------------------------------------------
-# Done
-
+# ESSAIS Vendredi 7 juin
+#------------------------------------------------------------------------------
 <tool id="gama_tool" name="gama" version="1.0.0b">
 
 8000 -> 6868
 
-=> tourne infini
+=> RES : tourne infini
 
 #------------------------------------------------------------------------------
-# Essai
 <tool id="gama_tool" name="gama" version="1.0.0j">
 
+(ajout de traces dans TTT.txt)
+
 -    /bin/bash cmd_gama_headless.sh > run_server.txt & sleep 20 && /bin/bash cmd_python_client.sh $nb_preys_init $nb_predators_init $nb_more_steps > run_client.txt;
 +    /bin/bash cmd_gama_headless.sh > run_server.txt & date > TTT.txt && sleep 300 && echo "fin sleep" >> TTT.txt && date >> TTT.txt && /bin/bash cmd_python_client.sh $nb_preys_init $nb_predators_init $nb_more_steps > run_client.txt;
 
-
-
+#------------------------------------------------------------------------------
+# ESSAIS Lundi 10 juin
 #------------------------------------------------------------------------------
 
+gama.def:
++  chmod -R 777 /opt
+
+<tool id="gama_tool" name="gama" version="1.0.0k">
+registry.forgemia.inra.fr/nathalie.rousse/use/gama:3fd4fb4b90db353af9bac01b99ee3b63220274c3
--- a/gama_tool.xml	Fri Jun 07 17:37:53 2024 +0000
+++ b/gama_tool.xml	Mon Jun 10 08:44:00 2024 +0000
@@ -1,11 +1,11 @@
-<tool id="gama_tool" name="gama" version="1.0.0j">
+<tool id="gama_tool" name="gama" version="1.0.0k">
 
   <description>tool for GAMA Platform</description>
 
   <requirements>
 
     <!-- singularity -->
-    <container type="singularity">oras://registry.forgemia.inra.fr/nathalie.rousse/use/gama:d01c3645810b3e5bf1b21170fd24d21fe1f831ec</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/nathalie.rousse/use/gama:3fd4fb4b90db353af9bac01b99ee3b63220274c3</container>
 
     <!-- image locale 
     <container type="singularity">/home/nrousse/workspace_git/SIWAA_regroup/USE_branch_gama/use/GAMA/containers/gama.simg</container -->
--- a/src/:wq	Fri Jun 07 17:37:53 2024 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,88 +0,0 @@
-<tool id="gama_tool" name="gama" version="1.0.0b">
-
-  <description>tool for GAMA Platform</description>
-
-  <requirements>
-
-    <!-- singularity -->
-    <container type="singularity">oras://registry.forgemia.inra.fr/nathalie.rousse/use/gama:d01c3645810b3e5bf1b21170fd24d21fe1f831ec</container>
-
-    <!-- image locale 
-    <container type="singularity">/home/nrousse/workspace_git/SIWAA_regroup/USE_branch_gama/use/GAMA/containers/gama.simg</container -->
-  </requirements>
-
-  <command detect_errors="aggressive">
-    <![CDATA[
-    cp -fr /opt/gama-platform .;
-    cp $__tool_directory__/src/MY_predatorPrey.gaml gama-platform/headless/samples/predatorPrey/.;
-    cp $__tool_directory__/src/MY_gama-headless.sh gama-platform/headless/.;
-    cp $__tool_directory__/src/MY_sequential_example.py .;
-    cp $__tool_directory__/src/cmd_gama_headless.sh .;
-    cp $__tool_directory__/src/cmd_python_client.sh .;
-    /bin/bash cmd_gama_headless.sh > run_server.txt & sleep 120 && /bin/bash cmd_python_client.sh $nb_preys_init $nb_predators_init $nb_more_steps > run_client.txt;
-    cp run_server.txt ${run_server_txt};
-    cp run_client.txt ${run_client_txt};
-    cp gama-platform/headless/samples/predatorPrey/results.txt ${results_txt};
-    ]]>
-  </command>
-
-  <inputs>
-
-    <param name="nb_preys_init" optional="true" type="integer"
-           value="200" min="0" max="1000"
-           label="nb_preys_init" help="[0, 1000]" />
-
-    <param name="nb_predators_init" optional="true" type="integer"
-           value="20" min="0" max="200"
-           label="nb_predators_init" help="[0, 200]" />
-
-    <param name="nb_more_steps" optional="true" type="integer"
-           value="10" min="4" max="100"
-           label="nb_more_steps" help="[4,100]" />
-
-  </inputs>
-
-  <outputs>
-    <data format="txt" name="run_server_txt" label="run_server_txt"/>
-    <data format="txt" name="run_client_txt" label="run_client_txt"/>
-    <data format="txt" name="results_txt" label="results_txt"/>
-  </outputs>
-
-  <tests>
-  </tests>
-
-  <help><![CDATA[
-
-Desc:
-
------
-
-gama_tool.xml tool running a GAMA Python client interacting with gama-server
-(Headless server) concerning a "Predator Prey" agent-based simulator.
-
-Code: MY_sequential_example.py
-
-Inputs:
-
-  - nb_preys_init
-  - nb_predators_init
-  - nb_more_steps
-
-Outputs:
-
-  - results_txt file (.txt) : produced while running the simulator
-    (cf 'reflex save_result' into MY_predatorPrey.gaml).
-  - run_server_txt file (.txt) : gama-server screen display capture
-  - run_client_txt file (.txt) : gama-client screen display capture
-
-Credits:
-
---------
-
--  Author: Nathalie Rousse nathalie.rousse@inrae.fr
--  Copyright: INRAE
-
-  ]]>
-  </help>
-
-</tool>