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117 lines
3.4 KiB
117 lines
3.4 KiB
13 years ago
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# Copyright 1999-2011 Gentoo Foundation
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# Distributed under the terms of the GNU General Public License v2
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# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.3.1_p4.ebuild,v 1.6 2011/10/20 08:46:56 xarthisius Exp $
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EAPI="4"
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inherit autotools eutils
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MY_PATCH="4"
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DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
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HOMEPAGE="http://emboss.sourceforge.net/"
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SRC_URI="
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ftp://${PN}.open-bio.org/pub/EMBOSS/old/${PV}/EMBOSS-${PV/_p${MY_PATCH}}.tar.gz
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ftp://${PN}.open-bio.org/pub/EMBOSS/old/${PV}/fixes/patches/patch-1-${MY_PATCH}.gz -> ${P}.patch.gz"
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LICENSE="GPL-2 LGPL-2"
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SLOT="0"
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KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
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IUSE="doc minimal mysql pdf png postgres static-libs X"
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DEPEND="
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dev-libs/expat
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dev-libs/libpcre:3
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sci-libs/plplot
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sys-libs/zlib
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mysql? ( dev-db/mysql )
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pdf? ( media-libs/libharu )
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png? (
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sys-libs/zlib
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media-libs/libpng
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media-libs/gd
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)
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postgres? ( dev-db/postgresql-base )
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!minimal? (
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sci-biology/primer3
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sci-biology/clustalw
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)
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X? ( x11-libs/libXt )"
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RDEPEND="${DEPEND}
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!sys-devel/cons"
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PDEPEND="
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!minimal? (
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sci-biology/aaindex
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sci-biology/cutg
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sci-biology/prints
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sci-biology/prosite
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sci-biology/rebase
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sci-biology/transfac
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)"
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S="${WORKDIR}/EMBOSS-${PV/_p${MY_PATCH}}"
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src_prepare() {
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epatch "${WORKDIR}"/${P}.patch
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epatch \
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"${FILESDIR}"/${PV}-unbundle-libs.patch
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eautoreconf
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}
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src_configure() {
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econf \
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$(use_with X x) \
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$(use_with png pngdriver "${EPREFIX}/usr") \
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$(use_with doc docroot "${EPREFIX}/usr") \
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$(use_with pdf hpdf "${EPREFIX}/usr") \
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$(use_with mysql mysql "${EPREFIX}/usr/bin/mysql_config") \
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$(use_with postgres postgresql "${EPREFIX}/usr/bin/pg_config") \
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$(use_enable amd64 64) \
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$(use_enable static-libs static) \
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--without-java \
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--enable-large \
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--enable-systemlibs \
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--includedir="${ED}/usr/include/emboss"
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}
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src_install() {
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einstall || die "Failed to install program files."
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dodoc AUTHORS ChangeLog FAQ NEWS README THANKS
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sed "s:EPREFIX:${EPREFIX}:g" "${FILESDIR}"/${PN}-README.Gentoo-2 > README.Gentoo && \
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dodoc README.Gentoo
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# Install env file for setting libplplot and acd files path.
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cat <<- EOF > 22emboss
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# plplot libs dir
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PLPLOT_LIB="${EPREFIX}/usr/share/EMBOSS/"
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# ACD files location
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EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd"
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EOF
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doenvd 22emboss
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# Symlink preinstalled docs to "/usr/share/doc".
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dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${PF}/manuals
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dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${PF}/programs
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dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials
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dosym /usr/share/EMBOSS/doc/html /usr/share/doc/${PF}/html
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# Clashes #330507
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mv "${ED}"/usr/bin/{digest,pepdigest} || die
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# Remove useless dummy files from the image.
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find emboss/data -name dummyfile -delete || die "Failed to remove dummy files."
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# Move the provided codon files to a different directory. This will avoid
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# user confusion and file collisions on case-insensitive file systems (see
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# bug #115446). This change is documented in "README.Gentoo".
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mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \
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die "Failed to move CODON directory."
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# Move the provided restriction enzyme prototypes file to a different name.
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# This avoids file collisions with versions of rebase that install their
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# own enzyme prototypes file (see bug #118832).
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mv "${ED}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \
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die "Failed to move enzyme equivalence file."
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}
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