# HG changeset patch
# User siwaa
# Date 1718013498 0
# Node ID 13296d4a29cf8ab1fa4e6bdeacfe35c2a79bc8ce
# Parent  614bed83ba5d7e6e56cd456883956c14d45e70c6
planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/gama/GAMA/galaxy-tools commit 927c1d94ea613d36a1b4b8d048ba21ad43a6f55e-dirty

diff -r 614bed83ba5d -r 13296d4a29cf ESSAISENCOURS.txt
--- a/ESSAISENCOURS.txt	Mon Jun 10 08:44:00 2024 +0000
+++ b/ESSAISENCOURS.txt	Mon Jun 10 09:58:18 2024 +0000
@@ -22,5 +22,35 @@
 gama.def:
 +  chmod -R 777 /opt
 
-<tool id="gama_tool" name="gama" version="1.0.0k">
+<tool id="gama_tool" name="gama" version="1.0.0k"> idem l
 registry.forgemia.inra.fr/nathalie.rousse/use/gama:3fd4fb4b90db353af9bac01b99ee3b63220274c3
+
+Singularity> echo $JAVA_HOME
+/opt/openjdk-17
+Singularity> which java
+/opt/openjdk-17/bin/java
+Singularity> java -version
+openjdk version "17-ea" 2021-09-14
+OpenJDK Runtime Environment (build 17-ea+14)
+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"
+
+
+
+
+
+
+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"
+  <run appl>
+
diff -r 614bed83ba5d -r 13296d4a29cf gama_tool.xml
--- a/gama_tool.xml	Mon Jun 10 08:44:00 2024 +0000
+++ b/gama_tool.xml	Mon Jun 10 09:58:18 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="gama_tool" name="gama" version="1.0.0k">
+<tool id="gama_tool" name="gama" version="1.0.0l">
 
   <description>tool for GAMA Platform</description>
 
diff -r 614bed83ba5d -r 13296d4a29cf src/MY_gama-headless.sh
--- a/src/MY_gama-headless.sh	Mon Jun 10 08:44:00 2024 +0000
+++ b/src/MY_gama-headless.sh	Mon Jun 10 09:58:18 2024 +0000
@@ -59,6 +59,20 @@
   passWork=.workspace$(find ./ -maxdepth 1 -name ".workspace*" | wc -l)
 fi
 
+
+
+
+#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 $memory -Djava.awt.headless=true org.eclipse.core.launcher.Main -configuration "$( 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.awt.headless=true org.eclipse.core.launcher.Main -configuration "$( dirname $( realpath "${BASH_SOURCE[0]}" ) )"/configuration -application msi.gama.headless.product -data $passWork "$@"; then