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113 lines
3.4 KiB
113 lines
3.4 KiB
# 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-6.0.1.ebuild,v 1.11 2011/10/20 08:46:56 xarthisius Exp $
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EAPI=1
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inherit eutils
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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="ftp://${PN}.open-bio.org/pub/EMBOSS/old/${PV}/EMBOSS-${PV}.tar.gz"
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LICENSE="GPL-2 LGPL-2"
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SLOT="0"
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KEYWORDS="amd64 ppc x86"
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IUSE="X png minimal"
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DEPEND="
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X? ( x11-libs/libXt )
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png? (
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sys-libs/zlib
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media-libs/libpng
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media-libs/gd
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)
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!minimal? (
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sci-biology/primer3
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sci-biology/clustalw
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)"
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RDEPEND="${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}"
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src_unpack() {
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unpack ${A}
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cd "${S}"
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epatch "${FILESDIR}"/${PN}-5.0.0-as-needed.patch
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local link_string="$(pkg-config --libs x11)"
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if use png; then
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link_string="${link_string} -lgd $(pkg-config --libs libpng)"
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fi
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sed -e "s:PATCH_PLPLOT:${link_string}:" -i plplot/Makefile.in \
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|| die "Failed to patch ajax Makefile"
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}
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src_compile() {
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local myconf
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myconf="--includedir=${D}/usr/include/emboss"
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use X || myconf="${EXTRA_CONF} --without-x"
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use png || myconf="${EXTRA_CONF} --without-pngdriver"
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econf ${myconf}
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# Do not install the JEMBOSS component (the --without-java configure option
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# does not work). JEMBOSS will eventually be available as a separate package.
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sed -i -e "s/SUBDIRS = plplot ajax nucleus emboss test doc jemboss/SUBDIRS = plplot ajax nucleus emboss test doc/" \
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Makefile || die
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emake || die
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}
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src_install() {
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einstall || die "Failed to install program files."
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dodoc AUTHORS ChangeLog FAQ NEWS README THANKS \
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|| die "Failed to install documentation."
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newdoc "${FILESDIR}"/${PN}-README.Gentoo-1 README.Gentoo \
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|| die "Failed to install Gentoo readme file."
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# Install env file for setting libplplot and acd files path.
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cat <<- EOF > 22emboss
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# plplot libs dir
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PLPLOT_LIB="/usr/share/EMBOSS/"
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# ACD files location
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EMBOSS_ACDROOT="/usr/share/EMBOSS/acd"
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EOF
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doenvd 22emboss || die "Failed to install environment file."
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# Symlink preinstalled docs to "/usr/share/doc".
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dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${PF}/manuals || die
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dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${PF}/programs || die
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dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials || die
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dosym /usr/share/EMBOSS/doc/html /usr/share/doc/${PF}/html || die
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# Clashes #330507
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mv "${D}"/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 "${D}"/usr/share/EMBOSS/data/CODONS{,.orig} || \
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die "Failed to move CODON directory."
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# Move the provided restriction enzyme prototypes file to a different name.
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# This avoids file collisions with versions of rebase that install their
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# own enzyme prototypes file (see bug #118832).
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mv "${D}"/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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