diff options
| -rw-r--r-- | sci-biology/emboss/ChangeLog | 6 | ||||
| -rw-r--r-- | sci-biology/emboss/emboss-4.0.0.ebuild | 90 | ||||
| -rw-r--r-- | sci-biology/emboss/emboss-6.0.1.ebuild | 8 | ||||
| -rw-r--r-- | sci-biology/emboss/emboss-6.1.0.ebuild | 11 |
4 files changed, 13 insertions, 102 deletions
diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog index 90f2d98ec775..e8760bce2b44 100644 --- a/sci-biology/emboss/ChangeLog +++ b/sci-biology/emboss/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-biology/emboss # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.63 2011/03/11 07:05:50 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.64 2011/04/04 16:01:13 jlec Exp $ + + 04 Apr 2011; Justin Lecher <jlec@gentoo.org> -emboss-4.0.0.ebuild, + emboss-6.0.1.ebuild, emboss-6.1.0.ebuild: + Dropped old, fix for wrong EAPI version, #361919 11 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4.ebuild, metadata.xml: diff --git a/sci-biology/emboss/emboss-4.0.0.ebuild b/sci-biology/emboss/emboss-4.0.0.ebuild deleted file mode 100644 index 7297831d5ffb..000000000000 --- a/sci-biology/emboss/emboss-4.0.0.ebuild +++ /dev/null @@ -1,90 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-4.0.0.ebuild,v 1.15 2011/03/09 19:50:38 armin76 Exp $ - -EAPI=1 - -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 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:1 - ) - !<dev-util/pscan-20000721-r1" - -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-${PV}" - -src_compile() { - local myconf - myconf="--includedir=${D}/usr/include/emboss" - use X || myconf="${EXTRA_CONF} --without-x" - use png || myconf="${EXTRA_CONF} --without-pngdriver" - - econf ${myconf} - # Do not install the JEMBOSS component (the --without-java configure option - # does not work). JEMBOSS will eventually be available as a separate package. - sed -i -e 's/SUBDIRS = plplot ajax nucleus emboss test doc jemboss/SUBDIRS = plplot ajax nucleus emboss test doc/' \ - Makefile || die - emake || die -} - -src_install() { - einstall || die "Failed to install program files." - - dodoc AUTHORS ChangeLog FAQ NEWS README THANKS "${FILESDIR}"/README.Gentoo \ - || die "Failed to install documentation." - - # Install env file for setting libplplot and acd files path. - doenvd "${FILESDIR}"/22emboss || die "Failed to install environment file." - - # Symlink preinstalled docs to /usr/share/doc. - dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${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/${PF}/html || die - - # Clashes #330507 - mv "${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 "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \ - die "Failed to move CODON directory." - - # Move the provided restriction enzyme prototypes file to a different name. - # This will avoid file collisions with future versions of rebase that will - # install their own enzyme prototypes file (see bug #118832). - mv "${ED}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \ - die "Failed to move enzyme equivalence file." -} diff --git a/sci-biology/emboss/emboss-6.0.1.ebuild b/sci-biology/emboss/emboss-6.0.1.ebuild index be91a23e12db..f36924bc3f82 100644 --- a/sci-biology/emboss/emboss-6.0.1.ebuild +++ b/sci-biology/emboss/emboss-6.0.1.ebuild @@ -1,6 +1,6 @@ # Copyright 1999-2011 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 1.8 2011/03/09 19:50:38 armin76 Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.0.1.ebuild,v 1.9 2011/04/04 16:01:13 jlec Exp $ EAPI=1 @@ -93,7 +93,7 @@ src_install() { dosym /usr/share/EMBOSS/doc/html /usr/share/doc/${PF}/html || die # Clashes #330507 - mv "${ED}"/usr/bin/{digest,pepdigest} || die + mv "${D}"/usr/bin/{digest,pepdigest} || die # Remove useless dummy files from the image. find emboss/data -name dummyfile -delete || die "Failed to remove dummy files." @@ -101,12 +101,12 @@ src_install() { # Move the provided codon files to a different directory. This will avoid # user confusion and file collisions on case-insensitive file systems (see # bug #115446). This change is documented in "README.Gentoo". - mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \ + mv "${D}"/usr/share/EMBOSS/data/CODONS{,.orig} || \ die "Failed to move CODON directory." # Move the provided restriction enzyme prototypes file to a different name. # This avoids file collisions with versions of rebase that install their # own enzyme prototypes file (see bug #118832). - mv "${ED}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \ + mv "${D}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \ die "Failed to move enzyme equivalence file." } diff --git a/sci-biology/emboss/emboss-6.1.0.ebuild b/sci-biology/emboss/emboss-6.1.0.ebuild index 9777fe2b24b7..a19181c548d8 100644 --- a/sci-biology/emboss/emboss-6.1.0.ebuild +++ b/sci-biology/emboss/emboss-6.1.0.ebuild @@ -1,6 +1,6 @@ # Copyright 1999-2011 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.ebuild,v 1.4 2011/03/09 19:50:38 armin76 Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.1.0.ebuild,v 1.5 2011/04/04 16:01:13 jlec Exp $ inherit eutils @@ -93,20 +93,17 @@ src_install() { die "Failed to remove duplicated documentation." # Remove useless dummy files from the image. - rm "${D}"/usr/share/EMBOSS/data/{AAINDEX,PRINTS,PROSITE,REBASE}/dummyfile \ - || die "Failed to remove dummy files." + find emboss/data -name dummyfile -delete || die "Failed to remove dummy files." # Move the provided codon files to a different directory. This will avoid # user confusion and file collisions on case-insensitive file systems (see # bug #115446). This change is documented in "README.Gentoo". - mv "${D}"/usr/share/EMBOSS/data/CODONS \ - "${D}"/usr/share/EMBOSS/data/CODONS.orig || \ + mv "${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 "${D}"/usr/share/EMBOSS/data/embossre.equ \ - "${D}"/usr/share/EMBOSS/data/embossre.equ.orig || \ + mv "${D}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \ die "Failed to move enzyme equivalence file." } |