[Bioperl-l] FreeBSD ports

[Mauricio Herrera Cuadra]

Fernan Aguero wrote:
> +----[ 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:
> http://portsmon.droso.net/portsconcordanceformaintainer.py?maintainer=fernan

Your welcome.

> 
> |  > - 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? 

Sure we can. What other subdirs of bioperl are more or less 
functional/stable, so they can be ported also? Perhaps bioperl-db and 
biosql-schema?

> 
> 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 totally agree with you. What do we need to bring it back?

> |  > 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.

Ok, so I better stop working on it. If you need any help please tell me 
George.

> | 
> | 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.
> 
> Great!
> 
> | I'll send all of this in as PR's and am happy to maintain them as
> | necessary.
> 
> OK.
> 
> | 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.

I'm also working on clustalx. Hope to send it soon.

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

Regards,

-- 
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Genética
Unidad de Morfofisiología y Función
Facultad de Estudios Superiores Iztacala, UNAM