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Nextflow launch script: improving search for JAVA_CMD #4830

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merged 4 commits into from
Mar 20, 2024
Merged

Nextflow launch script: improving search for JAVA_CMD #4830

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4f0cbfd
nextflow launch script: fix, point to get started guide, handle sdkma…
marcodelapierre Mar 20, 2024
aceb23a
nextflow script: removed sdkman case, message for java not found more…
marcodelapierre Mar 20, 2024
4f94833
Update nextflow [ci skip]
pditommaso Mar 20, 2024
b40c78f
Update nextflow [ci skip]
pditommaso Mar 20, 2024
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8 changes: 7 additions & 1 deletion nextflow
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Original file line number Diff line number Diff line change
Expand Up @@ -275,7 +275,7 @@ if [ ! -x "$JAVA_CMD" ] ; then
JAVA_CMD="$JAVA_HOME/bin/java"
fi
elif [ -x /usr/libexec/java_home ]; then
JAVA_CMD="$(/usr/libexec/java_home -v 1.8+)/bin/java"
JAVA_CMD="$(/usr/libexec/java_home -v 1.8+ 2>/dev/null)/bin/java" || JAVA_CMD=java
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else
JAVA_CMD="$(which java)" || JAVA_CMD=java
fi
Expand All @@ -288,7 +288,13 @@ if [ -f "$JAVA_KEY" ]; then
else
JAVA_VER="$("$JAVA_CMD" $NXF_OPTS -version 2>&1)"
if [ $? -ne 0 ]; then
getstarted_web="https://www.nextflow.io/docs/latest/getstarted.html"
echo_red "${JAVA_VER:-Failed to launch the Java virtual machine}"
echo_red "NOTE: Nextflow needs a Java virtual machine to run. To this end:
- make sure a \`java\` command can be found; or
- manually define the variables NXF_JAVA_HOME, JAVA_HOME or JAVA_CMD to point to an existing installation; or
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- install a Java virtual machine, for instance through https://sdkman.io (read the docs);
- for more details please refer to the Nextflow Get Started page at ${getstarted_web}."
echo_yellow "NOTE: Nextflow is trying to use the Java VM defined by the following environment variables:\n JAVA_CMD: $JAVA_CMD\n NXF_OPTS: $NXF_OPTS\n"
exit 1
fi
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