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Gentoo's Bugzilla – Attachment 176071 Details for
Bug 157827
[science overlay] new package: sci-biology/tgi-tools (seqclean, cdbfasta and friends)
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tgi-tools-0.2.ebuild
tgi-tools-0.1.ebuild (text/plain), 1.51 KB, created by
Martin Mokrejš
on 2008-12-21 19:14:16 UTC
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Description:
tgi-tools-0.2.ebuild
Filename:
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Creator:
Martin Mokrejš
Created:
2008-12-21 19:14:16 UTC
Size:
1.51 KB
patch
obsolete
># Copyright 1999-2008 Gentoo Foundation ># Distributed under the terms of the GNU General Public License v2 ># $Header: $ > >DESCRIPTION="The Gene Index Project utilities for genomic data processing: seqclean, cdbfasta, psx" >HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/" > >for i in seqclean/{seqclean,mdust,trimpoly} cdbfasta/cdbfasta tgicl/{psx,pvmsx,zmsort,tclust,sclust,nrcl,tgi_cpp_library}; do > SRC_URI="${SRC_URI} ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/${i}.tar.gz" >done > >LICENSE="Artistic" >SLOT="0" >IUSE="pvm" >KEYWORDS="~x86" > >DEPEND="pvm? ( sys-cluster/pvm )" >RDEPEND="${DEPEND}" > >S=${WORKDIR} > >src_unpack() { > unpack {seqclean,mdust,trimpoly,cdbfasta,tgi_cpp_library}.tar.gz > for i in nrcl sclust tclust zmsort psx pvmsx; do > mkdir "${S}"/${i} > cd "${S}" > unpack ${i}.tar.gz > done >} > >src_compile() { > sed -i 's/use Mailer;/#use Mailer;/' seqclean/seqclean > sed -i 's/-V\t\tverbose/-V\t\tverbose\\/' zmsort/zmsort.cpp > # TODO: fix error in nrcl > for i in cdbfasta mdust psx sclust tclust trimpoly zmsort $(use pvm && echo pvmsx); do > sed -i 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' \ > ${S}/${i}/Makefile > cd "${S}/${i}" || die "cd ${i} failed" > emake || die "emake failed in ${i}" > done >} > >src_install() { > dobin cdbfasta/{cdbfasta,cdbyank} seqclean/{seqclean,cln2qual,bin/seqclean.psx} > for i in mdust psx sclust tclust trimpoly zmsort $(use pvm && echo pvmsx); do > dobin ${i}/${i} > done > for i in cdbfasta seqclean; do > newdoc ${i}/README README.${i} > done >}
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bug 157827
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103797
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176071
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177530
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237789