diff options
| -rw-r--r-- | sci-biology/embassy-mse/ChangeLog | 6 | ||||
| -rw-r--r-- | sci-biology/embassy-mse/embassy-mse-1.0.0-r5.ebuild | 19 | ||||
| -rw-r--r-- | sci-biology/embassy-signature/ChangeLog | 6 | ||||
| -rw-r--r-- | sci-biology/embassy-signature/embassy-signature-0.1.0-r2.ebuild | 13 | ||||
| -rw-r--r-- | sci-biology/embassy-structure/ChangeLog | 6 | ||||
| -rw-r--r-- | sci-biology/embassy-structure/embassy-structure-0.1.0-r2.ebuild | 13 | ||||
| -rw-r--r-- | sci-biology/embassy-topo/ChangeLog | 6 | ||||
| -rw-r--r-- | sci-biology/embassy-topo/embassy-topo-1.0.0-r4.ebuild | 13 | ||||
| -rw-r--r-- | sci-biology/embassy-vienna/ChangeLog | 6 | ||||
| -rw-r--r-- | sci-biology/embassy-vienna/embassy-vienna-1.6.ebuild | 13 | ||||
| -rw-r--r-- | sci-biology/emboss/ChangeLog | 5 | ||||
| -rw-r--r-- | sci-biology/emboss/emboss-5.0.0.ebuild | 104 |
12 files changed, 29 insertions, 181 deletions
diff --git a/sci-biology/embassy-mse/ChangeLog b/sci-biology/embassy-mse/ChangeLog index 42189bc05354..041ca9da03f6 100644 --- a/sci-biology/embassy-mse/ChangeLog +++ b/sci-biology/embassy-mse/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-biology/embassy-mse # Copyright 2000-2008 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-mse/ChangeLog,v 1.29 2008/08/27 19:39:51 ribosome Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-mse/ChangeLog,v 1.30 2008/08/27 21:49:38 ribosome Exp $ + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + -embassy-mse-1.0.0-r5.ebuild: + Pruning version that will never be stabilised. *embassy-mse-1.0.0-r6 (27 Aug 2008) diff --git a/sci-biology/embassy-mse/embassy-mse-1.0.0-r5.ebuild b/sci-biology/embassy-mse/embassy-mse-1.0.0-r5.ebuild deleted file mode 100644 index bf43585300e0..000000000000 --- a/sci-biology/embassy-mse/embassy-mse-1.0.0-r5.ebuild +++ /dev/null @@ -1,19 +0,0 @@ -# Copyright 1999-2007 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-mse/embassy-mse-1.0.0-r5.ebuild,v 1.2 2007/08/07 18:37:50 ribosome Exp $ - -EBOV="5.0.0" - -inherit embassy - -DESCRIPTION="EMBOSS integrated version of MSE - Multiple Sequence Screen Editor" -SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${EBOV}.tar.gz - mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" - -KEYWORDS="~amd64 ~ppc ~sparc ~x86" - -src_install() { - embassy_src_install - insinto /usr/include/emboss/mse - doins h/*.h -} diff --git a/sci-biology/embassy-signature/ChangeLog b/sci-biology/embassy-signature/ChangeLog index e4021971b13d..aa6d37fb5816 100644 --- a/sci-biology/embassy-signature/ChangeLog +++ b/sci-biology/embassy-signature/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-biology/embassy-signature # Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-signature/ChangeLog,v 1.14 2008/08/27 19:55:11 ribosome Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-signature/ChangeLog,v 1.15 2008/08/27 21:53:10 ribosome Exp $ + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + -embassy-signature-0.1.0-r2.ebuild: + Pruning version that will never be stabilised. *embassy-signature-0.1.0-r3 (27 Aug 2008) diff --git a/sci-biology/embassy-signature/embassy-signature-0.1.0-r2.ebuild b/sci-biology/embassy-signature/embassy-signature-0.1.0-r2.ebuild deleted file mode 100644 index 1d7243979af2..000000000000 --- a/sci-biology/embassy-signature/embassy-signature-0.1.0-r2.ebuild +++ /dev/null @@ -1,13 +0,0 @@ -# Copyright 1999-2007 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-signature/embassy-signature-0.1.0-r2.ebuild,v 1.1 2007/07/18 01:53:11 ribosome Exp $ - -EBOV="5.0.0" - -inherit embassy - -DESCRIPTION="Protein signature add-on package for EMBOSS" -SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${EBOV}.tar.gz - mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" - -KEYWORDS="~amd64 ~ppc ~sparc ~x86" diff --git a/sci-biology/embassy-structure/ChangeLog b/sci-biology/embassy-structure/ChangeLog index 9f3ab2a4e636..e2ae5c0e2746 100644 --- a/sci-biology/embassy-structure/ChangeLog +++ b/sci-biology/embassy-structure/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-biology/embassy-structure # Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-structure/ChangeLog,v 1.14 2008/08/27 20:39:11 ribosome Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-structure/ChangeLog,v 1.15 2008/08/27 21:54:41 ribosome Exp $ + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + -embassy-structure-0.1.0-r2.ebuild: + Pruning version that will never be stabilised. *embassy-structure-0.1.0-r3 (27 Aug 2008) diff --git a/sci-biology/embassy-structure/embassy-structure-0.1.0-r2.ebuild b/sci-biology/embassy-structure/embassy-structure-0.1.0-r2.ebuild deleted file mode 100644 index c15c728276ae..000000000000 --- a/sci-biology/embassy-structure/embassy-structure-0.1.0-r2.ebuild +++ /dev/null @@ -1,13 +0,0 @@ -# Copyright 1999-2007 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-structure/embassy-structure-0.1.0-r2.ebuild,v 1.1 2007/07/18 01:54:57 ribosome Exp $ - -EBOV="5.0.0" - -inherit embassy - -DESCRIPTION="Protein structure add-on package for EMBOSS" -SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${EBOV}.tar.gz - mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" - -KEYWORDS="~amd64 ~ppc ~sparc ~x86" diff --git a/sci-biology/embassy-topo/ChangeLog b/sci-biology/embassy-topo/ChangeLog index a5484272e341..256f6a20664d 100644 --- a/sci-biology/embassy-topo/ChangeLog +++ b/sci-biology/embassy-topo/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-biology/embassy-topo # Copyright 2000-2008 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-topo/ChangeLog,v 1.24 2008/08/27 19:33:10 ribosome Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-topo/ChangeLog,v 1.25 2008/08/27 21:55:59 ribosome Exp $ + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + -embassy-topo-1.0.0-r4.ebuild: + Pruning version that will never be stabilised. *embassy-topo-1.0.0-r5 (27 Aug 2008) diff --git a/sci-biology/embassy-topo/embassy-topo-1.0.0-r4.ebuild b/sci-biology/embassy-topo/embassy-topo-1.0.0-r4.ebuild deleted file mode 100644 index b0832f0fdf6c..000000000000 --- a/sci-biology/embassy-topo/embassy-topo-1.0.0-r4.ebuild +++ /dev/null @@ -1,13 +0,0 @@ -# Copyright 1999-2007 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-topo/embassy-topo-1.0.0-r4.ebuild,v 1.1 2007/07/18 01:56:22 ribosome Exp $ - -EBOV="5.0.0" - -inherit embassy - -DESCRIPTION="EMBOSS integrated version of TOPO - Transmembrane protein display" -SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${EBOV}.tar.gz - mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" - -KEYWORDS="~amd64 ~ppc ~sparc ~x86" diff --git a/sci-biology/embassy-vienna/ChangeLog b/sci-biology/embassy-vienna/ChangeLog index 10f0322ac79e..ebd0edf6aea7 100644 --- a/sci-biology/embassy-vienna/ChangeLog +++ b/sci-biology/embassy-vienna/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-biology/embassy-vienna # Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-vienna/ChangeLog,v 1.3 2008/08/27 19:34:55 ribosome Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-vienna/ChangeLog,v 1.4 2008/08/27 21:58:00 ribosome Exp $ + + 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> + -embassy-vienna-1.6.ebuild: + Pruning version that will never be stabilised. *embassy-vienna-1.7.2 (27 Aug 2008) diff --git a/sci-biology/embassy-vienna/embassy-vienna-1.6.ebuild b/sci-biology/embassy-vienna/embassy-vienna-1.6.ebuild deleted file mode 100644 index 4b802771227c..000000000000 --- a/sci-biology/embassy-vienna/embassy-vienna-1.6.ebuild +++ /dev/null @@ -1,13 +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/embassy-vienna/embassy-vienna-1.6.ebuild,v 1.2 2008/08/27 17:42:19 ribosome Exp $ - -EBOV="5.0.0" - -inherit embassy - -DESCRIPTION="EMBOSS integrated version of the Vienna RNA package - RNA folding" -SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${EBOV}.tar.gz - mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz" - -KEYWORDS="~amd64 ~ppc ~sparc ~x86" 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." -} |