[Bioperl-l] environment variables (et al.) for bioperl-run tests

Amir Karger akarger at CGR.Harvard.edu
Tue Jan 6 16:00:40 UTC 2009

We just installed Bioperl-run on a cluster with very limited environment
variables. So a huge number of tests failed.

I would *really* appreciate it if the wiki had info on which environment
variables need to be set for all the Bioperl::Run::* packages so that
./Build test will work. Since it would be a pretty big job for any one
person, perhaps somebody can make a page (or an area of
http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix or maybe
http://www.bioperl.org/wiki/Run_package with links back & forth) with
spaces for all the modules, and each module's maintainer can put in
their one or two environment variables? It would make my life and the
life of many others a lot easier than having to read every package's

Thanks in advance,

-Amir Karger
Life Sciences Research Computing, FAS IT
Harvard University

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