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authorJustin Lecher <jlec@gentoo.org>2012-04-26 16:35:43 +0000
committerJustin Lecher <jlec@gentoo.org>2012-04-26 16:35:43 +0000
commit2c4c1211426a2d068f7b90804a5c6437c0591e4c (patch)
treefc856966a88b9d24db60f7c33d89c8e28b281c5b /sci-biology/emboss
parentsci-astronomy/sextractor: Move to EAPI=4 and autotools-util.eclass, Cleaned old (diff)
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sci-biology/emboss: Drop old
(Portage version: 2.2.0_alpha101/cvs/Linux x86_64)
Diffstat (limited to 'sci-biology/emboss')
-rw-r--r--sci-biology/emboss/ChangeLog7
-rw-r--r--sci-biology/emboss/emboss-6.1.0.ebuild109
2 files changed, 5 insertions, 111 deletions
diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
index fcf6d0203801..fd0dd9332695 100644
--- a/sci-biology/emboss/ChangeLog
+++ b/sci-biology/emboss/ChangeLog
@@ -1,6 +1,9 @@
# 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 1.66 2011/10/20 08:46:56 xarthisius Exp $
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.67 2012/04/26 16:35:43 jlec Exp $
+
+ 26 Apr 2012; Justin Lecher <jlec@gentoo.org> -emboss-6.1.0.ebuild:
+ Drop old
20 Oct 2011; Kacper Kowalik <xarthisius@gentoo.org> emboss-6.3.1_p4.ebuild,
emboss-6.1.0.ebuild, emboss-6.1.0-r1.ebuild, emboss-6.0.1.ebuild:
diff --git a/sci-biology/emboss/emboss-6.1.0.ebuild b/sci-biology/emboss/emboss-6.1.0.ebuild
deleted file mode 100644
index 012f5c43628a..000000000000
--- a/sci-biology/emboss/emboss-6.1.0.ebuild
+++ /dev/null
@@ -1,109 +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-6.1.0.ebuild,v 1.7 2011/10/20 08:46:56 xarthisius Exp $
-
-inherit eutils
-
-DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
-HOMEPAGE="http://emboss.sourceforge.net/"
-SRC_URI="ftp://${PN}.open-bio.org/pub/EMBOSS/old/${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-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/${PF}/html || die
-
- # Remove frestdist documentation conflicting with the EMBASSY philypnew
- # package.
- rm "${D}"/usr/share/EMBOSS/doc/programs/text/frestdist.txt || \
- die "Failed to remove duplicated documentation."
-
- # 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."
-}