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changeset 16:4117e2f0a591 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 12:02:59 +0000
parents 5667e00be2aa
children 5a94c8c7c8cc
files ESSAISENCOURS.txt gama_tool.xml src/.MY_gama-headless.sh.swp src/MY_gama-headless.sh
diffstat 4 files changed, 23 insertions(+), 32 deletions(-) [+]
line wrap: on
line diff
--- a/ESSAISENCOURS.txt	Mon Jun 10 10:38:08 2024 +0000
+++ b/ESSAISENCOURS.txt	Mon Jun 10 12:02:59 2024 +0000
@@ -22,11 +22,11 @@
 gama.def:
 +  chmod -R 777 /opt
 
-<tool id="gama_tool" name="gama" version="1.0.0n">
+<tool id="gama_tool" name="gama" version="1.0.0o">
 
     registry.forgemia.inra.fr/nathalie.rousse/use/gama:3fd4fb4b90db353af9bac01b99ee3b63220274c3
 
-    /bin/bash cmd_gama_headless.sh > run_server.txt & date > TTT.txt && sleep 600 && 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;
+    /bin/bash cmd_gama_headless.sh > run_server.txt & date > TTT.txt && sleep 400 && 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;
 
 Singularity> echo $JAVA_HOME
 /opt/openjdk-17
@@ -38,22 +38,11 @@
 OpenJDK 64-Bit Server VM (build 17-ea+14, mixed mode, sharing)
 
 vim MY_gama-headless.sh :
-#lun10juin
 MY_JAVA_DIR=./_java
-mkdir -p ./_java/.systemPrefs
-mkdir -p ./_java/.userPrefs
-#chmod -R 755 ./_java
-chmod -R 777 ./_java
-#export JAVA_OPTS="-Djava.util.prefs.systemRoot=./_java -Djava.util.prefs.userRoot=./_java/.userPrefs"
-if ! java -cp "$( dirname $( realpath "${BASH_SOURCE[0]}" ) )"/../plugins/org.eclipse.equinox.launcher*.jar -Xms512m $memory -Djava.io.tmpdir=$MY_TEMP_DIR -Djava.util.prefs.systemRoot=./_java -Djava.util.prefs.userRoot=./_java/.userPrefs -Djava.awt.headless=true org.eclipse.core.launcher.Main -configuration "$( dirname $( realpath "${BASH_SOURCE[0]}" ) )"/configuration -application msi.gama.headless.product -data $passWork "$@"; then
-
+...
+echo "TRACE MY_gama-headless.sh: pwd:"
+pwd;
+pwd > RRR.txt
 
+if ! java -cp "$( dirname $( realpath "${BASH_SOURCE[0]}" ) )"/../plugins/org.eclipse.equinox.launcher*.jar -Xms512m $memory -Djava.io.tmpdir=$MY_TEMP_DIR -Djava.util.prefs.systemRoot=${MY_JAVA_DIR} -Djava.util.prefs.userRoot=${MY_JAVA_USER_PREFS_DIR} -Djava.awt.headless=true org.eclipse.core.launcher.Main -configuration "$( dirname $( realpath "${BASH_SOURCE[0]}" ) )"/configuration -application msi.gama.headless.product -data $passWork "$@"; then
 
-        SOURCES
-        mkdir -p ~/.java/.systemPrefs
-        mkdir ~/.java/.userPrefs
-        chmod -R 755 ~/.java
-        export JAVA_OPTS="-Djava.util.prefs.systemRoot=/home/user/.java -Djava.util.prefs.userRoot=/home/user/.java/.userPrefs"
-        SOURCE AUTRE
-        ./jmeter -Djava.util.prefs.systemRoot=/home/youruser/.jmeter -Djava.util.prefs.userRoot=/home/youruser/.jmeter/.userPrefs
-
--- a/gama_tool.xml	Mon Jun 10 10:38:08 2024 +0000
+++ b/gama_tool.xml	Mon Jun 10 12:02:59 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="gama_tool" name="gama" version="1.0.0n">
+<tool id="gama_tool" name="gama" version="1.0.0o">
 
   <description>tool for GAMA Platform</description>
 
@@ -19,7 +19,7 @@
     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 600 && 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;
+    /bin/bash cmd_gama_headless.sh > run_server.txt & date > TTT.txt && sleep 400 && 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 ${results_txt};
Binary file src/.MY_gama-headless.sh.swp has changed
--- a/src/MY_gama-headless.sh	Mon Jun 10 10:38:08 2024 +0000
+++ b/src/MY_gama-headless.sh	Mon Jun 10 12:02:59 2024 +0000
@@ -59,23 +59,25 @@
   passWork=.workspace$(find ./ -maxdepth 1 -name ".workspace*" | wc -l)
 fi
 
+#if ! java -cp "$( dirname $( realpath "${BASH_SOURCE[0]}" ) )"/../plugins/org.eclipse.equinox.launcher*.jar -Xms512m $memory -Djava.awt.headless=true org.eclipse.core.launcher.Main -configuration "$( dirname $( realpath "${BASH_SOURCE[0]}" ) )"/configuration -application msi.gama.headless.product -data $passWork "$@"; then
 
+MY_JAVA_DIR=./_java
+MY_JAVA_SYSTEM_PREFS_DIR=${MY_JAVA_DIR}/.systemPrefs
+MY_JAVA_USER_PREFS_DIR=${MY_JAVA_DIR}/.userPrefs
+mkdir -p ${MY_JAVA_DIR}
+mkdir -p ${MY_JAVA_SYSTEM_PREFS_DIR}
+mkdir -p ${MY_JAVA_USER_PREFS_DIR}
+chmod -R 777 ${MY_JAVA_DIR}
+
+MY_TEMP_DIR=.
 
 
-#lun10juin
-MY_JAVA_DIR=./_java
-mkdir -p ./_java/.systemPrefs
-mkdir -p ./_java/.userPrefs
-#chmod -R 755 ./_java
-chmod -R 777 ./_java
-#export JAVA_OPTS="-Djava.util.prefs.systemRoot=./_java -Djava.util.prefs.userRoot=./_java/.userPrefs"
+echo "TRACE MY_gama-headless.sh: pwd:"
+pwd;
+pwd > RRR.txt
 
 
-
-
-#if ! java -cp "$( dirname $( realpath "${BASH_SOURCE[0]}" ) )"/../plugins/org.eclipse.equinox.launcher*.jar -Xms512m $memory -Djava.awt.headless=true org.eclipse.core.launcher.Main -configuration "$( dirname $( realpath "${BASH_SOURCE[0]}" ) )"/configuration -application msi.gama.headless.product -data $passWork "$@"; then
-MY_TEMP_DIR=.
-if ! java -cp "$( dirname $( realpath "${BASH_SOURCE[0]}" ) )"/../plugins/org.eclipse.equinox.launcher*.jar -Xms512m $memory -Djava.io.tmpdir=$MY_TEMP_DIR -Djava.util.prefs.systemRoot=./_java -Djava.util.prefs.userRoot=./_java/.userPrefs -Djava.awt.headless=true org.eclipse.core.launcher.Main -configuration "$( dirname $( realpath "${BASH_SOURCE[0]}" ) )"/configuration -application msi.gama.headless.product -data $passWork "$@"; then
+if ! java -cp "$( dirname $( realpath "${BASH_SOURCE[0]}" ) )"/../plugins/org.eclipse.equinox.launcher*.jar -Xms512m $memory -Djava.io.tmpdir=$MY_TEMP_DIR -Djava.util.prefs.systemRoot=${MY_JAVA_DIR} -Djava.util.prefs.userRoot=${MY_JAVA_USER_PREFS_DIR} -Djava.awt.headless=true org.eclipse.core.launcher.Main -configuration "$( dirname $( realpath "${BASH_SOURCE[0]}" ) )"/configuration -application msi.gama.headless.product -data $passWork "$@"; then
     echo "Error in you command, here's the log :"
     cat $passWork/.metadata/.log
     exit 1