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ssadedin / bpipe

Bpipe - a tool for running and managing bioinformatics pipelines
http://docs.bpipe.org/
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PBSpro wrapper, missing option #160

Open marchoeppner opened 9 years ago

marchoeppner commented 9 years ago

Hi,

sorry, pbspro issues again ;) The following line should be added to the wrapper:

PBS -V

This will automatically export environment variables. Otherwise, one would have to always specify full paths to everything. Since we use environment modules" to load software, exporting $PATH and other variables is needed. If permanently adding this is not desirable, may add some optional argument that can be passed on to pbspro?

Cheers, Marc

ssadedin commented 9 years ago

It sounds like we definitely want to support that. I think it needs to be optional, there has been some discussion about it before.

I'll look at adding this option.

marchoeppner commented 9 years ago

Thanks. I think the discussion you pointed out is missing some details. While it is true that specifying full paths can avoid confusion with respect to software versions etc, this should also be addressed through the use of a properly maintained tool database. The other issue is that while I can certainly write out full paths to certain binaries, this does not address issues with other variables, including PERL5LIB, LD_LIBRARY_PATH etc. So dismissing "-V" as being unprofessional or whatever is perhaps missing the point.

Actually, come to think of it, built-in support for environment modules would be awesome (I'll post something on that over on the google group).