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#1 2004-05-11 13:59:23

arch_newb
Member
From: Canada
Registered: 2004-04-27
Posts: 24

bioperl

Hi all,
I would like to request that bioperl be added to the package list.
The sources can be found at

http://www.bioperl.org/Core/Latest/index.shtml

The install doc is here
http://bioperl.org/Core/Latest/INSTALL
Based on the install docs I am not sure if its worth making into a package or not. Could someone experienced in making packages please advise on this.

thanks for your help
Cheers
arch_newb

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#2 2004-05-11 15:06:13

dp
Member
From: Zürich, Switzerland
Registered: 2003-05-27
Posts: 3,366
Website

Re: bioperl

:-)

actually i was working on bioperl (core) and as it's working for about 2 weeks on my machine, i think the testing is over and it is time to make it available to archlinux

:-)

... soon ... in some hours hopefully, i will include it in extra


The impossible missions are the only ones which succeed.

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#3 2004-05-11 15:40:13

arch_newb
Member
From: Canada
Registered: 2004-04-27
Posts: 24

Re: bioperl

dp wrote:

:-)

actually i was working on bioperl (core) and as it's working for about 2 weeks on my machine, i think the testing is over and it is time to make it available to archlinux

:-)

... soon ... in some hours hopefully, i will include it in extra

Dude thats awesome.
Have U got any of the other bioperl modules working (db,run,ext,microarray, etc...)?
Cheers
arch_newb

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#4 2004-05-11 15:59:35

dp
Member
From: Zürich, Switzerland
Registered: 2003-05-27
Posts: 3,366
Website

Re: bioperl

arch_newb wrote:

Dude thats awesome.
Have U got any of the other bioperl modules working (db,run,ext,microarray, etc...)?

no, unfortunately not in detail

-run and -ext should be easy to do too, but -db needs a db running i think (what is difficult to make a pkg of - if needed)

-microarray is big, but should work too

you can play around with it ... should be very simmilar to the -core:

# $Id: PKGBUILD,v 1.1 2004/05/11 15:34:18 damir Exp $
# Maintainer: damir <damir@archlinux.org>
pkgname=bioperl
pkgver=1.4
pkgrel=1
pkgdesc="Bioperl is a collection of perl modules that facilitate the development of perl scripts for bioinformatics applications."
url="http://www.bioperl.org"
depends=('perl')

source=($url/DIST/$pkgname-$pkgver.tar.gz)
build() {
  cd $startdir/src/$pkgname-$pkgver
  yes a | perl Makefile.PL
  make || return 1
  make DESTDIR=$startdir/pkg install

    mv $startdir/pkg/usr/lib/perl5/site_perl/?.?.? $startdir/pkg/usr/lib/perl5/site_perl/current
  rm -rf $startdir/pkg/usr/lib/perl5/?.?.?
}
md5sums=('5ef3e6e824c3f444e788d7fc9bda1fcb')

The impossible missions are the only ones which succeed.

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