diff options
| -rw-r--r-- | sci-biology/emboss/Manifest | 3 | ||||
| -rw-r--r-- | sci-biology/emboss/emboss-6.0.1.ebuild | 112 | ||||
| -rw-r--r-- | sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild | 117 |
3 files changed, 0 insertions, 232 deletions
diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest index c364f2c77e86..42ec06043003 100644 --- a/sci-biology/emboss/Manifest +++ b/sci-biology/emboss/Manifest @@ -1,4 +1 @@ -DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d -DIST EMBOSS-6.3.1.tar.gz 23572243 SHA256 4f3290600a970c2a23a7e47f884d1fc8156ec40538f7191a6e83e23680d27a8d DIST EMBOSS-6.6.0.tar.gz 117962028 SHA256 7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e SHA512 2d28a03381f7dc98d205aa50202fbbac02ad218fc775d86579d310296be124403623484b1907154d915f15cd32a9f8cf16ecfaa6c4a28b362e24dc8e6380b75a WHIRLPOOL 25241e865b1ad4e5459f84a2b0def7cd00a6e2904db714838dfe0533e01f8373cfdd4c78df225f9d2a77ead4cb9998791bd19f46b32e220810ad950fa288b9fe -DIST emboss-6.3.1_p4.patch.gz 4070 SHA256 61d1b62e3148541d496103711db6526ba76488a0899af2c98264b03bf8d6e24c diff --git a/sci-biology/emboss/emboss-6.0.1.ebuild b/sci-biology/emboss/emboss-6.0.1.ebuild deleted file mode 100644 index 0edfd7a639d0..000000000000 --- a/sci-biology/emboss/emboss-6.0.1.ebuild +++ /dev/null @@ -1,112 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=1 - -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-${PV}.tar.gz" -LICENSE="GPL-2 LGPL-2" - -SLOT="0" -KEYWORDS="amd64 ppc x86" -IUSE="X png minimal" - -DEPEND=" - X? ( x11-libs/libXt ) - png? ( - sys-libs/zlib - media-libs/libpng - media-libs/gd - ) - !minimal? ( - sci-biology/primer3 - sci-biology/clustalw - )" - -RDEPEND="${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_unpack() { - unpack ${A} - cd "${S}" - 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_compile() { - local myconf - myconf="--includedir=${D}/usr/include/emboss" - use X || myconf="${EXTRA_CONF} --without-x" - use png || myconf="${EXTRA_CONF} --without-pngdriver" - - econf ${myconf} - # Do not install the JEMBOSS component (the --without-java configure option - # does not work). JEMBOSS will eventually be available as a separate package. - sed -i -e "s/SUBDIRS = plplot ajax nucleus emboss test doc jemboss/SUBDIRS = plplot ajax nucleus emboss test doc/" \ - Makefile || die - emake || die -} - -src_install() { - einstall || die "Failed to install program files." - - dodoc AUTHORS ChangeLog FAQ NEWS README THANKS \ - || die "Failed to install documentation." - newdoc "${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/${PF}/html || die - - # Clashes #330507 - mv "${D}"/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 "${D}"/usr/share/EMBOSS/data/CODONS{,.orig} || \ - die "Failed to move CODON directory." - - # Move the provided restriction enzyme prototypes file to a different name. - # This avoids file collisions with versions of rebase that install their - # own enzyme prototypes file (see bug #118832). - mv "${D}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \ - die "Failed to move enzyme equivalence file." -} diff --git a/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild b/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild deleted file mode 100644 index e8baba4c7752..000000000000 --- a/sci-biology/emboss/emboss-6.3.1_p4-r1.ebuild +++ /dev/null @@ -1,117 +0,0 @@ -# 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." -} |