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Diffstat (limited to 'sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild')
| -rw-r--r-- | sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild | 117 |
1 files changed, 117 insertions, 0 deletions
diff --git a/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild b/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild new file mode 100644 index 000000000000..e8baba4c7752 --- /dev/null +++ b/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild @@ -0,0 +1,117 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="4" + +inherit autotools eutils + +MY_PATCH="4" + +DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package" +HOMEPAGE="http://emboss.sourceforge.net/" +SRC_URI=" + ftp://${PN}.open-bio.org/pub/EMBOSS/old/${PV}/EMBOSS-${PV/_p${MY_PATCH}}.tar.gz + ftp://${PN}.open-bio.org/pub/EMBOSS/old/${PV}/fixes/patches/patch-1-${MY_PATCH}.gz -> ${P}.patch.gz" + +LICENSE="GPL-2 LGPL-2" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" +IUSE="doc minimal mysql pdf png postgres static-libs X" + +DEPEND=" + dev-libs/expat + dev-libs/libpcre:3 + sci-libs/plplot + sys-libs/zlib + mysql? ( virtual/mysql ) + pdf? ( media-libs/libharu ) + png? ( + sys-libs/zlib + media-libs/libpng + media-libs/gd + ) + postgres? ( dev-db/postgresql ) + !minimal? ( + sci-biology/primer3 + sci-biology/clustalw + ) + X? ( x11-libs/libXt )" +RDEPEND="${DEPEND} + !sys-devel/cons" +PDEPEND=" + !minimal? ( + sci-biology/aaindex + sci-biology/cutg + sci-biology/prints + sci-biology/prosite + sci-biology/rebase + sci-biology/transfac + )" + +S="${WORKDIR}/EMBOSS-${PV/_p${MY_PATCH}}" + +src_prepare() { + epatch "${WORKDIR}"/${P}.patch + epatch \ + "${FILESDIR}"/${PV}-unbundle-libs.patch \ + "${FILESDIR}/${PF}_plcol.patch" + eautoreconf +} + +src_configure() { + econf \ + $(use_with X x) \ + $(use_with png pngdriver "${EPREFIX}/usr") \ + $(use_with doc docroot "${EPREFIX}/usr") \ + $(use_with pdf hpdf "${EPREFIX}/usr") \ + $(use_with mysql mysql "${EPREFIX}/usr/bin/mysql_config") \ + $(use_with postgres postgresql "${EPREFIX}/usr/bin/pg_config") \ + $(use_enable amd64 64) \ + $(use_enable static-libs static) \ + --without-java \ + --enable-large \ + --enable-systemlibs \ + --includedir="${ED}/usr/include/emboss" +} + +src_install() { + einstall || die "Failed to install program files." + + dodoc AUTHORS ChangeLog FAQ NEWS README THANKS + sed "s:EPREFIX:${EPREFIX}:g" "${FILESDIR}"/${PN}-README.Gentoo-2 > README.Gentoo && \ + dodoc README.Gentoo + + # Install env file for setting libplplot and acd files path. + cat <<- EOF > 22emboss + # plplot libs dir + PLPLOT_LIB="${EPREFIX}/usr/share/EMBOSS/" + # ACD files location + EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd" + EOF + doenvd 22emboss + + # Symlink preinstalled docs to "/usr/share/doc". + dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${PF}/manuals + dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${PF}/programs + dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials + dosym /usr/share/EMBOSS/doc/html /usr/share/doc/${PF}/html + + # Clashes #330507 + mv "${ED}"/usr/bin/{digest,pepdigest} || die + + # Remove useless dummy files from the image. + find emboss/data -name dummyfile -delete || die "Failed to remove dummy files." + + # Move the provided codon files to a different directory. This will avoid + # user confusion and file collisions on case-insensitive file systems (see + # bug #115446). This change is documented in "README.Gentoo". + mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \ + die "Failed to move CODON directory." + + # Move the provided restriction enzyme prototypes file to a different name. + # This avoids file collisions with versions of rebase that install their + # own enzyme prototypes file (see bug #118832). + mv "${ED}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \ + die "Failed to move enzyme equivalence file." +} |