Pileus Git - ~andy/sunrise/blob - sci-biology/tgi-tools/tgi-tools-0.1.ebuild

   1 # Copyright 1999-2006 Gentoo Foundation
   2 # Distributed under the terms of the GNU General Public License v2
   3 # $Header: $
   4
   5 DESCRIPTION="The Gene Index Project utilities for genomic data processing: seqclean, cdbfasta, psx"
   6 HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"
   7
   8 for i in seqclean/{seqclean,mdust,trimpoly} cdbfasta/cdbfasta tgicl/{psx,pvmsx,zmsort,tclust,sclust,nrcl,tgi_cpp_library}; do
   9         SRC_URI="${SRC_URI} ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/${i}.tar.gz"
  10 done
  11
  12 LICENSE="Artistic"
  13 SLOT="0"
  14 IUSE="pvm"
  15 KEYWORDS="~x86"
  16
  17 DEPEND="pvm? ( sys-cluster/pvm )"
  18 RDEPEND=${DEPEND}
  19
  20 RESTRICT="mirror"
  21
  22 S=${WORKDIR}
  23
  24 src_unpack() {
  25         unpack {seqclean,mdust,trimpoly,cdbfasta,tgi_cpp_library}.tar.gz
  26         for i in nrcl sclust tclust zmsort psx pvmsx; do
  27                 mkdir "${S}"/${i}
  28                 cd "${S}"/${i}
  29                 unpack ${i}.tar.gz
  30         done
  31 }
  32
  33 src_compile() {
  34         sed -i 's/use Mailer;/#use Mailer;/' ${S}/seqclean/seqclean
  35         sed -i 's/-V\t\tverbose/-V\t\tverbose\\/' ${S}/zmsort/zmsort.cpp
  36         # TODO: fix error in nrcl
  37         for i in cdbfasta mdust psx sclust tclust trimpoly zmsort $(use pvm && echo pvmsx); do
  38                 sed -i 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' ${S}/${i}/Makefile
  39                 cd ${S}/${i} || die "cd ${i} failed"
  40                 emake || die "emake failed in ${i}"
  41         done
  42 }
  43
  44 src_install() {
  45         dobin cdbfasta/{cdbfasta,cdbyank} seqclean/{seqclean,cln2qual,bin/seqclean.psx}
  46         for i in mdust psx sclust tclust trimpoly zmsort $(use pvm && echo pvmsx); do
  47                 dobin ${i}/${i}
  48         done
  49         for i in cdbfasta seqclean; do
  50                 newdoc ${i}/README README.${i}
  51         done
  52 }