diff options
| -rw-r--r-- | sci-biology/emboss/ChangeLog | 5 | ||||
| -rw-r--r-- | sci-biology/emboss/emboss-5.0.0.ebuild | 104 |
2 files changed, 4 insertions, 105 deletions
diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog index 067bf042faf8..f13d735f091e 100644 --- a/sci-biology/emboss/ChangeLog +++ b/sci-biology/emboss/ChangeLog @@ -1,6 +1,9 @@ # 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 1.48 2008/08/27 21:28:36 ribosome Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.49 2008/08/27 21:59:28 ribosome Exp $ + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> -emboss-5.0.0.ebuild: + Pruning version that will never be stabilised. 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> emboss-4.0.0.ebuild: Depend on ClustalW 1.83 since version 2.x will soon be added to Portage diff --git a/sci-biology/emboss/emboss-5.0.0.ebuild b/sci-biology/emboss/emboss-5.0.0.ebuild deleted file mode 100644 index 7dc99b1a7050..000000000000 --- a/sci-biology/emboss/emboss-5.0.0.ebuild +++ /dev/null @@ -1,104 +0,0 @@ -# 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-5.0.0.ebuild,v 1.2 2008/01/25 23:51:41 markusle 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 "${FILESDIR}"/${P}-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." -} |