I recently ran into a problem where the tool-dependency env.sh file was not getting sourced for a particular tool. I realized that the problem was in how the tool 'requirement' tag was specified. The requirement tag was specified as in the Tool Config Syntax documentation (http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Crequirement...): <requirements> <requirement type="binary">taxBuilder</requirement> </requirements> However, it appears that the type must be set to "package" in order for the dependency system to source the env.sh file (http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies): <requirements> <requirement type="package">taxBuilder</requirement> </requirements> I'm working on getting this working with bedtools, and I'm wondering what the recommended way to do this would be. Since there are various binaries for this package, I'm thinking I could do something like: <requirements> <requirement type="package">bedtools</requirement> <requirement type="binary">genomeCoverageBed</requirement> </requirements> Secondly, once this is sorted out, it would be nice to update the Tool Config Syntax documentation. Thanks in advance for any advice. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University