Just to make sure - since it hasn't been explicitly stated - is this tool being installed from the tool shed? The environment variable setup in tool_dependencies.xml will only be available for tool shed installs. You will also need a special requirement in your tool to make it available (https://github.com/bgruening/galaxytools/blob/master/augustus/augustus.xml#L...). I consider this whole approach very heavy and not robust given that it is explicitly tied to the tool shed. If there is any way you can explicitly target the next release with your code there is a much better solution to this problem - you can use $__tool_directory__ to reference the directory tools are installed in (https://bitbucket.org/galaxy/galaxy-central/commits/ddbe0d12bc86da406bb96213...). It works for tool shed installations and tools just directly loaded into Galaxy - it also doesn't require you to setup anything special in tool_dependencies.xml or the requirements section. It is a cheetah variable instead of a runtime environment variable so need to escape the $ either. If you are on an older version of Galaxy - the diff above is pretty small - you should be possible to backport this enhancement locally with minimal effort. Hope this helps, -John On Thu, Feb 26, 2015 at 8:35 AM, Pierre Lindenbaum <pierre.lindenbaum@univ-nantes.fr> wrote:
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 :
<sanitizer> <valid initial="string.printable"> <remove value="'"/> </valid> </sanitizer>
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
P.
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