Sorry I wasn't clear about that - it hasn't reached galaxy-dist yet -
you can download the latest snapshot of 15.03 release (I believe it is
running on usegalaxy.org as of yesterday) via this link instead
https://bitbucket.org/galaxy/galaxy-central/get/release_15.03.zip.

Also not need to escape $__tool_directory__  (so use
$__tool_directory__ instead of \$__tool_directory__).

-John

On Thu, Feb 26, 2015 at 9:40 AM, Pierre Lindenbaum
<pierre.lindenb...@univ-nantes.fr> wrote:
> On 02/26/2015 02:51 PM, John Chilton wrote:
>>
>> 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.
>
>
> no, my future plan is to put it in the tool shed but for now, I'm just
> trying to make it run in my local instance of galaxy.
>
> I'm sorry if that wasn't clear.
>
>
> I've just downloaded the latest version of galaxy via
> https://bitbucket.org/galaxy/galaxy-dist/get/tip.zip (
> galaxy-galaxy-dist-02ddea42faad.zip )
> and re-tried.
>
>
> I tried to print the variable $__tool_directory__ with the tool.xml below
>
> but it's not defined
>
> $ cat /tmp/error7.txt
> dir= .
> Error: Could not find or load main class
> com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS
>
>
> the xml:
>
>    <?xml version="1.0"?>
>    <tool hidden="false"
>    id="com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS"
>    version="1.0.0" name="vcffilterjs">
>       <requirements>
>         <requirement type="binary">java</requirement>
>       </requirements>
>
>       <command><![CDATA[echo "dir=\$__tool_directory__ ." >
>    /tmp/error7.txt && java -cp
>
> \$__tool_directory__/commons-jexl-2.1.1.jar:\$__tool_directory__/commons-logging-1.1.1.jar:\$__tool_directory__/htsjdk-1.129.jar:\$__tool_directory__/snappy-java-1.0.3-rc3.jar:\$__tool_directory__/vcffilterjs.jar
>    com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS -e
>    '${expression}' -o ${output} ${input}  2>> /tmp/error7.txt ]]></command>
>       <inputs>
>             <param format="vcf" name="input" type="data" label="VCF
>    input"/>
>             <param name="expression" type="text" label="javascript
>    expression">
>                 <sanitizer>
>                          <valid initial="string.printable">
>                  <remove value="&apos;"/>
>             </valid>
>                 </sanitizer>
>             </param>
>
>         </inputs>
>       <outputs>
>             <data format="vcf" name="output"/>
>         </outputs>
>       <stdio>
>         <exit_code range="1:"/>
>         <exit_code range=":-1"/>
>       </stdio>
>       <help></help>
>    </tool>
>
>
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