diff options
| -rw-r--r-- | sci-biology/emboss/ChangeLog | 7 | ||||
| -rw-r--r-- | sci-biology/emboss/emboss-6.0.1.ebuild | 104 |
2 files changed, 110 insertions, 1 deletions
diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog index 1de7d18f5144..f352634a7764 100644 --- a/sci-biology/emboss/ChangeLog +++ b/sci-biology/emboss/ChangeLog @@ -1,6 +1,11 @@ # ChangeLog for sci-biology/emboss # Copyright 2000-2008 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.46 2008/01/25 23:51:41 markusle Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.47 2008/08/26 18:51:27 ribosome Exp $ + +*emboss-6.0.1 (26 Aug 2008) + + 26 Aug 2008; Olivier Fisette <ribosome@gentoo.org> +emboss-6.0.1.ebuild: + New upstream version. 25 Jan 2008; Markus Dittrich <markusle@gentoo.org> +files/emboss-5.0.0-as-needed.patch, emboss-4.0.0.ebuild, diff --git a/sci-biology/emboss/emboss-6.0.1.ebuild b/sci-biology/emboss/emboss-6.0.1.ebuild new file mode 100644 index 000000000000..2e4169213d31 --- /dev/null +++ b/sci-biology/emboss/emboss-6.0.1.ebuild @@ -0,0 +1,104 @@ +# Copyright 1999-2008 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.0.1.ebuild,v 1.1 2008/08/26 18:51:27 ribosome Exp $ + +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" +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 + )" + +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_unpack() { + unpack ${A} + cd "${S}" + 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_compile() { + EXTRA_CONF="--includedir=${D}/usr/include/emboss" + ! use X && EXTRA_CONF="${EXTRA_CONF} --without-x" + ! use png && EXTRA_CONF="${EXTRA_CONF} --without-pngdriver" + + econf ${EXTRA_CONF} || die + # Do not install the JEMBOSS component (the --without-java configure option + # does not work). JEMBOSS will eventually be available as a separate package. + sed -i -e "s/SUBDIRS = plplot ajax nucleus emboss test doc jemboss/SUBDIRS = plplot ajax nucleus emboss test doc/" \ + Makefile || die + emake || die +} + +src_install() { + einstall || die "Failed to install program files." + + dodoc AUTHORS ChangeLog FAQ NEWS README THANKS \ + || die "Failed to install documentation." + newdoc "${FILESDIR}"/${PN}-README.Gentoo-1 README.Gentoo \ + || die "Failed to install Gentoo readme file." + + # Install env file for setting libplplot and acd files path. + cat <<- EOF > 22emboss + # plplot libs dir + PLPLOT_LIB="/usr/share/EMBOSS/" + # ACD files location + EMBOSS_ACDROOT="/usr/share/EMBOSS/acd" + EOF + doenvd 22emboss || die "Failed to install environment file." + + # Symlink preinstalled docs to "/usr/share/doc". + dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${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/${PF}/html || die + + # Remove useless dummy files from the image. + rm "${D}"/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 "${D}"/usr/share/EMBOSS/data/CODONS \ + "${D}"/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 "${D}"/usr/share/EMBOSS/data/embossre.equ \ + "${D}"/usr/share/EMBOSS/data/embossre.equ.orig || \ + die "Failed to move enzyme equivalence file." +} |