[Bioperl-l] FreeBSD ports

Fernan Aguero fernan at iib.unsam.edu.ar
Thu Sep 29 14:30:54 EDT 2005

+----[ George Hartzell <hartzell at kestrel.alerce.com> (29.Sep.2005 14:24):
| 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 ;) )

Thanks for the help! I'm maintaining a number of ports,
besides bioperl:

|  > - 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 was about to ask the same question. Maybe we can
coordinate our efforts and/or help each other in the
maintainance of these ports and to add new ports? 

If other bioperl-l@ readers are using FreeBSD and want to
volunteer, speak up. No previous experience required, we can
get you started quickly :)

I'm also afraid that this discussion doesn't belong to
bioperl-l@ so perhaps we should seek to bring freebsd-bio@
to live again?

|  > 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...).

thanks for the fasta3 update :) I've been fighting with it
for some time and never got to finish it 

| 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
| necessary.


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

I've been working on ports for mpiblast, poa/poaviz, the
vienna RNA package, codonw and wemboss, but time has been
scarce as of late.

But definitely we should have this discussion in freebsd-bio@
or some other place that is both FreeBSD AND bio specific :)



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