# Copyright 1999-2014 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.1.0-r1.ebuild,v 1.7 2014/07/30 01:12:51 grknight Exp $ EAPI="3" inherit eutils 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-${PV}.tar.gz" LICENSE="GPL-2 LGPL-2" SLOT="0" KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" IUSE="X png minimal" DEPEND=" X? ( x11-libs/libXt ) png? ( sys-libs/zlib media-libs/libpng media-libs/gd ) !minimal? ( sci-biology/primer3 sci-biology/clustalw )" RDEPEND="${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}" src_prepare() { epatch "${FILESDIR}"/${PN}-5.0.0-as-needed.patch local link_string="$(pkg-config --libs x11)" if use png; then link_string="${link_string} -lgd $(pkg-config --libs libpng)" fi sed -e "s:PATCH_PLPLOT:${link_string}:" -i plplot/Makefile.in \ || die "Failed to patch ajax Makefile" } src_configure() { local myconf myconf="--includedir=${ED}/usr/include/emboss" use X || myconf="${EXTRA_CONF} --without-x" use png || myconf="${EXTRA_CONF} --without-pngdriver" econf ${myconf} # Do not install the JEMBOSS component (the --without-java configure option # does not work). JEMBOSS will eventually be available as a separate package. sed -i -e "s/SUBDIRS = plplot ajax nucleus emboss test doc jemboss/SUBDIRS = plplot ajax nucleus emboss test doc/" \ Makefile || die } src_install() { einstall || die "Failed to install program files." dodoc AUTHORS ChangeLog FAQ NEWS README THANKS \ || die "Failed to install documentation." newdoc "${FILESDIR}"/${PN}-README.Gentoo-1 README.Gentoo \ || die "Failed to install Gentoo readme file." # Install env file for setting libplplot and acd files path. cat <<- EOF > 22emboss # plplot libs dir PLPLOT_LIB="${EPREFIX}/usr/share/EMBOSS/" # ACD files location EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd" EOF doenvd 22emboss || die "Failed to install environment file." # Symlink preinstalled docs to "/usr/share/doc". dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${PF}/manuals || die dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${PF}/programs || die dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials || die dosym /usr/share/EMBOSS/doc/html /usr/share/doc/${PF}/html || die # Remove frestdist documentation conflicting with the EMBASSY philypnew # package. rm "${ED}"/usr/share/EMBOSS/doc/programs/text/frestdist.txt || \ die "Failed to remove duplicated documentation." # 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." }