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="'"/> </valid> </sanitizer> </param> </inputs> <outputs> <data format="vcf" name="output"/> </outputs> <stdio> <exit_code range="1:"/> <exit_code range=":-1"/> </stdio> <help></help> </tool>