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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