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#L6).

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/ddbe0d12bc86da406bb96213e23b8ddb273ed669).
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.lindenb...@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="&apos;"/>
>                 </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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