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

Chris Fields cjfields at illinois.edu
Tue Jan 6 16:58:40 UTC 2009

This is on the agenda for the BioPerl-run 1.6 release.  We have a bug  
tracking this:


Feel free to add your own test results to this as an attachment; I'll  
probably start working on that this week.


On Jan 6, 2009, at 10:00 AM, Amir Karger wrote:

> 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
> documentation.
> Thanks in advance,
> -Amir Karger
> Life Sciences Research Computing, FAS IT
> Harvard University
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> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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