I’m working on a very simple tool. <tool id="gc_stat" name="GC Stat" version="0.1.0"> <requirements> <requirement type="binary">Rscript</requirement> <requirement type="package" version="1.1">samtools</requirement> <requirement type="package" version="3.0.3">R</requirement> </requirements> <stdio> <exit_code range="1:" /> </stdio> <command><![CDATA[ samtools view $bam | Rscript simple_script.R > $output ]]></command> <inputs> <param name='bam' type='data' format='bam' label='Mapped reads' help='BAM files'/> </inputs> <outputs> <data format='tabular' name='output' label='GC Statistic on ${on_string}'/> </outputs> <help><![CDATA[ Calculates a GC statistic for the specified BAM file. ]]></help> </tool> this won’t work because Rscript is not running in the tool install directory and can’t find simple_script.R… I’ve just been reading https://trello.com/c/9lQ7Sr8I/636-galaxy-tool-enhancement-to-accommodate-rep... and it seems that I have to add another file… <?xml version="1.0"?> <tool_dependency> <set_environment version="1.0"> <environment_variable name="TOOL_INSTALL_DIR" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> </set_environment> </tool_dependency> and add a set_enviornment dependency to bring it in. <requirements> ... <requirement type="set_environment">TOOL_INSTALL_DIR</requirement> </requirements> <command><![CDATA[ samtools view $bam | Rscript $TOOL_INSTALL_DIR/simple_script.R > $output ]]></command> I did that but the tool still won’t execute, in fact the . Maybe because I have to put this into a toolshed - or maybe I’ve done something wrong? I think this complexity could be avoided by setting an TOOL_INSTALL_DIR environment var as a tool is executed (though John doesn’t seem to like that idea due to a responsibility mixing issue) I think it’s a worthy goal to make tool development as frictionless as possible. Is there a simpler way to do this? Brad