diff options
| -rw-r--r-- | sci-biology/emboss/ChangeLog | 11 | ||||
| -rw-r--r-- | sci-biology/emboss/emboss-6.1.0-r1.ebuild | 110 |
2 files changed, 119 insertions, 2 deletions
diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog index 4ca45c3a1162..de2ba5b04b60 100644 --- a/sci-biology/emboss/ChangeLog +++ b/sci-biology/emboss/ChangeLog @@ -1,6 +1,13 @@ # ChangeLog for sci-biology/emboss -# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.54 2009/09/01 21:57:55 ribosome Exp $ +# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.55 2010/03/07 20:58:42 jlec Exp $ + +*emboss-6.1.0-r1 (07 Mar 2010) + + 07 Mar 2010; Justin Lecher (jlec) <jlec@gentoo.org> + +emboss-6.1.0-r1.ebuild: + Moved to EAPI=3 for PREFIX support, imported prefix patches from overlay, + keyworded as in overlay 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: Giving up maintainership of this package. diff --git a/sci-biology/emboss/emboss-6.1.0-r1.ebuild b/sci-biology/emboss/emboss-6.1.0-r1.ebuild new file mode 100644 index 000000000000..485e5d25ddcd --- /dev/null +++ b/sci-biology/emboss/emboss-6.1.0-r1.ebuild @@ -0,0 +1,110 @@ +# Copyright 1999-2010 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 1.1 2010/03/07 20:58:42 jlec 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://${PN}.open-bio.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz" +LICENSE="GPL-2 LGPL-2" + +SLOT="0" +KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~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="${DEPEND}" + +PDEPEND="!minimal? ( + sci-biology/aaindex + sci-biology/cutg + sci-biology/prints + sci-biology/prosite + >=sci-biology/rebase-707 + sci-biology/transfac + )" + +S="${WORKDIR}/EMBOSS-${PV}" + +src_prepare() { + epatch "${FILESDIR}"/${PN}-5.0.0-as-needed.patch + + local link_string="-lX11"; + if use png; then + link_string="${link_string} -lgd -lpng" + fi + sed -e "s:PATCH_PLPLOT:${link_string}:" -i plplot/Makefile.in \ + || die "Failed to patch ajax Makefile" +} + +src_configure() { + EXTRA_CONF="--includedir=${ED}/usr/include/emboss" + ! use X && EXTRA_CONF="${EXTRA_CONF} --without-x" + ! use png && EXTRA_CONF="${EXTRA_CONF} --without-pngdriver" + + econf ${EXTRA_CONF} || die + # Do not install the JEMBOSS component (the --without-java configure option + # does not work). JEMBOSS will eventually be available as a separate package. + sed -i -e "s/SUBDIRS = plplot ajax nucleus emboss test doc jemboss/SUBDIRS = plplot ajax nucleus emboss test doc/" \ + Makefile || die +} + +src_install() { + einstall || die "Failed to install program files." + + dodoc AUTHORS ChangeLog FAQ NEWS README THANKS \ + || die "Failed to install documentation." + newdoc "${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." + + # Remove useless dummy files from the image. + rm "${ED}"/usr/share/EMBOSS/data/{AAINDEX,PRINTS,PROSITE,REBASE}/dummyfile \ + || die "Failed to remove dummy files." + + # Move the provided codon files to a different directory. This will avoid + # user confusion and file collisions on case-insensitive file systems (see + # bug #115446). This change is documented in "README.Gentoo". + mv "${ED}"/usr/share/EMBOSS/data/CODONS \ + "${ED}"/usr/share/EMBOSS/data/CODONS.orig || \ + die "Failed to move CODON directory." + + # Move the provided restriction enzyme prototypes file to a different name. + # This avoids file collisions with versions of rebase that install their + # own enzyme prototypes file (see bug #118832). + mv "${ED}"/usr/share/EMBOSS/data/embossre.equ \ + "${ED}"/usr/share/EMBOSS/data/embossre.equ.orig || \ + die "Failed to move enzyme equivalence file." +} |