[Bioperl-l] Bioperl NT update
Thu, 14 Dec 2000 14:41:17 -0800
Hilmar Lapp wrote:
> Shailesh L Mistry wrote:
> > The other minor problems relate to programs that I do not have on my machine
> > specifically blast, clustalw and TCoffee.
> > Do I assume that only people who use these programs should worry about the
> > testing of them or will they definitely be part of the distribution?
> I guess they will, however many people will not use every part. Still, if
> you want to take the effort and get all those programs installed (as far as
> they are available for NT), that'd be great. I'm wondering whether the
> respective modules can live with a precomputed output, too. Peter?
The test scripts for the clustalw.pm, standaloneblast.pm and tcoffee.pm
modules check for the presence of the respective underlying programs
they need on the host machine when in a Unix (or Linux) environment. If
they are not found, the respective tests are skipped. However, under NT
this approach is untested and probably won’t work. I suspect the
underlying programs may not even be available under NT (or Mac).
I think the best bet would be to completely skip all the tests relating
to these modules unless the host OS is a Unix variant. Alternatively,
the tests could presumably live with precomputed output to be used if
the Bioperl installation test-harness detects a non-unix environment .
However I do not know how to incorporate either of these approaches in
the Bioperl installation. Can anyone help?