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.3E_tag_set):

<requirement type="binary">taxBuilder</requirement>

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):

<requirement type="package">taxBuilder</requirement>

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:

<requirement type="package">bedtools</requirement>
<requirement type="binary">genomeCoverageBed</requirement>

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

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