[Bioperl-l] FreeBSD ports

George Hartzell hartzell at kestrel.alerce.com
Thu Sep 29 13:02:09 EDT 2005

Mauricio Herrera Cuadra writes:
 > Due to the recent threads about the FreeBSD ports, I've come up with 
 > some questions:
 > - Fernán: are you working only on p5-bioperl? (I've sent XML::DOM::XPath 
 > a few weeks ago, so you have one less dependency to worry about ;) )
 > - George: are you planning to send/maintain p5-bioperl-run and 
 > p5-bioperl-devel (and their respective dependencies)?
 > - Anyone else is preparing ports for FreeBSD?
 > I'm working on p5-bioperl-ext (and its dependencies). I hope to have it 
 > ready for the 1.6.0 release.

I have ports and/or updates for p5-bioperl-devel and p5-bioperl-run
(been using them for a while now, updating for 1.5.1), tidying up one
for exonerate (making sure it passes everything w/ assertions
enabled), fasta3 (update), and first drafts for mdust and seg
(pains-in-the-ass because of how the src files are made available on
the web...).

I have an almost working -ext, except that it was splatting it's libs
in odd places and I was in a hurry, so I just put them where they
belonged by hand.

Depending on how stable the location of the "release candidate" is for
wise 2.2.3-rc7 (in other words, if Ewan doesn't object), I'll roll up
a wise-devel port to support p5-bioperl-run.

I'll send all of this in as PR's and am happy to maintain them as

I'm happy to build others if folks suggest them and as time allows.


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