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

   1 # Copyright 1999-2008 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="${DEPEND}"
  19
  20 S=${WORKDIR}
  21
  22 src_unpack() {
  23         unpack {seqclean,mdust,trimpoly,cdbfasta,tgi_cpp_library}.tar.gz
  24         for i in nrcl sclust tclust zmsort psx pvmsx; do
  25                 mkdir "${S}"/${i}
  26                 cd "${S}"/${i}
  27                 unpack ${i}.tar.gz
  28         done
  29 }
  30
  31 src_compile() {
  32         sed -i 's/use Mailer;/#use Mailer;/' seqclean/seqclean
  33         sed -i 's/-V\t\tverbose/-V\t\tverbose\\/' zmsort/zmsort.cpp
  34         # TODO: fix error in nrcl
  35         for i in cdbfasta mdust psx sclust tclust trimpoly zmsort $(use pvm && echo pvmsx); do
  36                 sed -i 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' \
  37                         ${i}/Makefile
  38                 cd "${S}/${i}" || die "cd ${i} failed"
  39                 emake || die "emake failed in ${i}"
  40         done
  41 }
  42
  43 src_install() {
  44         dobin cdbfasta/{cdbfasta,cdbyank} seqclean/{seqclean,cln2qual,bin/seqclean.psx}
  45         for i in mdust psx sclust tclust trimpoly zmsort $(use pvm && echo pvmsx); do
  46                 dobin ${i}/${i}
  47         done
  48         for i in cdbfasta seqclean; do
  49                 newdoc ${i}/README README.${i}
  50         done
  51 }