> You'll need to white list the semi-colon which Galaxy has replaced as a security precaution (user free text can be exploited). See <sanitizer> here: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Peter

Thanks: adding :

              <valid initial="string.printable">
                     <remove value="&apos;"/>

fixed the probem.

> Could you confirm if the environment variable is being set now?

Hum the variable is not set , I've changed <command> to

<command><![CDATA[echo "JVARKITDIR=\$JVARKITDIR expression=${expression} " > /tmp/error7.txt && java -cp \$JVARKITDIR/commons-jexl-2.1.1.jar:\$JVARKITDIR/commons-logging-1.1.1.jar:\$JVARKITDIR/htsjdk-1.129.jar:\$JVARKITDIR/snappy-java-1.0.3-rc3.jar:\$JVARKITDIR/vcffilterjs.jar com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS -e '${expression}' -o ${output} ${input} 2>> /tmp/error7.txt ]]>

here is the content of tmp/error7.txt

$ cat /tmp/error7.txt
JVARKITDIR= expression=variant!=null;
Error: Could not find or load main class com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS

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