Dan and Greg,

SnpEff is an example of a java based tool in the tooshed that would be good to be able to deploy without any editing by the installer. 

Pablo has hardcoded the path to the jar and config files in the tool_config:   /Users/pablocingolani/snpEff/
With directions for the installer to change that path.

Would it be possible to supply the install path of a tool to the tool's cheetah command/config templating in a similar way that $__tool_data_path__ is provided?
   $__tool_path__
If a tool had dependencies could those be provided as a dict?
    $__tool_dependencies__['samtools']

Then snpEff  command could be:
<command>java -Xmx6G -jar $__tool_path__/snpEff.jar eff -c $__tool_path__/snpEff.config
-i $inputFormat -o $outputFormat -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command>
 
This could allow for tool versioning
and be used for for the common java packaging technique of an executable jar
with META_DATA that references dependencies in a relative dir, usually ./lib/

Thanks,

JJ



Browse snpeff revision c052639fa666 (repository tip)
hg clone http://jjohnson@toolshed.g2.bx.psu.edu/repos/pcingola/snpeff