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):
<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
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