From: "Justin Lecher" <jlec@gentoo.org>
To: gentoo-commits@lists.gentoo.org
Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/mira/
Date: Tue, 22 May 2012 19:43:15 +0000 (UTC) [thread overview]
Message-ID: <1337713671.5d074abd7b1d4ea82db2fd5ea860ac8f9afd80cb.jlec@gentoo> (raw)
commit: 5d074abd7b1d4ea82db2fd5ea860ac8f9afd80cb
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue May 22 19:07:51 2012 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue May 22 19:07:51 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5d074abd
sci-biology/mira: Add missing eutils.eclass, bump to EAPI=4, remove usage of base.eclass; drop old
(Portage version: 2.2.0_alpha107/git/Linux x86_64, unsigned Manifest commit)
---
sci-biology/mira/ChangeLog | 7 +++-
sci-biology/mira/mira-3.2.1-r2.ebuild | 57 -----------------------------
sci-biology/mira/mira-3.2.1.17-r1.ebuild | 57 -----------------------------
sci-biology/mira/mira-3.2.1.20.ebuild | 58 ------------------------------
sci-biology/mira/mira-3.4.0.1.ebuild | 27 ++++++++------
5 files changed, 22 insertions(+), 184 deletions(-)
diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog
index 0982f99..4cd234f 100644
--- a/sci-biology/mira/ChangeLog
+++ b/sci-biology/mira/ChangeLog
@@ -1,7 +1,12 @@
# ChangeLog for sci-biology/mira
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 22 May 2012; Justin Lecher <jlec@gentoo.org> -mira-3.2.1-r2.ebuild,
+ -mira-3.2.1.17-r1.ebuild, -mira-3.2.1.20.ebuild, mira-3.4.0.1.ebuild:
+ Add missing eutils.eclass, bump to EAPI=4, remove usage of base.eclass; drop
+ old
+
*mira-3.4.0.1 (08 Dec 2011)
08 Dec 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/mira/mira-3.2.1-r2.ebuild b/sci-biology/mira/mira-3.2.1-r2.ebuild
deleted file mode 100644
index c110959..0000000
--- a/sci-biology/mira/mira-3.2.1-r2.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-MIRA_3RDPARTY_PV="17-04-2010"
-
-inherit autotools base multilib
-
-DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina"
-HOMEPAGE="http://www.chevreux.org/projects_mira.html"
-SRC_URI="mirror://sourceforge/mira-assembler/${P}.tar.bz2
- mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-
-CDEPEND=">=dev-libs/boost-1.41.0-r3
- dev-util/google-perftools"
-DEPEND="${CDEPEND}
- dev-libs/expat"
-RDEPEND="${CDEPEND}
- sci-biology/smalt-bin
- sci-biology/ssaha2-bin"
-
-src_prepare() {
- find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die
- epatch "${FILESDIR}"/${PN}-3.0.0-asneeded.patch
- # http://sourceforge.net/apps/trac/mira-assembler/ticket/47
- epatch "${FILESDIR}"/mira_left_clip.readpool.C.patch
- epatch "${FILESDIR}"/libtool.m4.patch
- AT_M4DIR="config/m4" eautoreconf
-}
-
-src_configure() {
- econf \
- --with-boost="${EPREFIX}"/usr/$(get_libdir) \
- --with-boost-libdir="${EPREFIX}"/usr/$(get_libdir) \
- --with-boost-thread=boost_thread-mt
-}
-
-src_compile() {
- base_src_compile
- # TODO: resolve docbook incompatibility for building docs
- if use doc; then emake -C doc clean docs || die; fi
-}
-
-src_install() {
- einstall || die
- dodoc AUTHORS GETTING_STARTED NEWS README* HELP_WANTED THANKS INSTALL
- find doc/docs/man -type f | xargs doman
- find doc/docs/texinfo -type f | xargs doinfo
- dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
-}
diff --git a/sci-biology/mira/mira-3.2.1.17-r1.ebuild b/sci-biology/mira/mira-3.2.1.17-r1.ebuild
deleted file mode 100644
index 04b3767..0000000
--- a/sci-biology/mira/mira-3.2.1.17-r1.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-MIRA_3RDPARTY_PV="17-04-2010"
-
-inherit autotools base multilib
-
-DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina"
-HOMEPAGE="http://www.chevreux.org/projects_mira.html"
-SRC_URI="mirror://sourceforge/mira-assembler/${P}.tar.bz2
- mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-
-CDEPEND=">=dev-libs/boost-1.41.0-r3
- dev-util/google-perftools"
-DEPEND="${CDEPEND}
- dev-libs/expat"
-RDEPEND="${CDEPEND}
- sci-biology/smalt-bin
- sci-biology/ssaha2-bin"
-
-src_prepare() {
- find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die
- epatch "${FILESDIR}"/${PN}-3.0.0-asneeded.patch
- # http://sourceforge.net/apps/trac/mira-assembler/ticket/47
- epatch "${FILESDIR}"/mira_left_clip.readpool.C.patch
- epatch "${FILESDIR}"/libtool.m4.patch
- AT_M4DIR="config/m4" eautoreconf
-}
-
-src_configure() {
- econf \
- --with-boost="${EPREFIX}"/usr/$(get_libdir) \
- --with-boost-libdir="${EPREFIX}"/usr/$(get_libdir) \
- --with-boost-thread=boost_thread-mt
-}
-
-src_compile() {
- base_src_compile
- # TODO: resolve docbook incompatibility for building docs
- if use doc; then emake -C doc clean docs || die "This will probably die because upstream did not imrove re-genartion of the docs yet."; fi
-}
-
-src_install() {
- einstall || die
- dodoc AUTHORS GETTING_STARTED NEWS README* HELP_WANTED THANKS INSTALL
- find doc/docs/man -type f | xargs doman
- find doc/docs/texinfo -type f | xargs doinfo
- dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
-}
diff --git a/sci-biology/mira/mira-3.2.1.20.ebuild b/sci-biology/mira/mira-3.2.1.20.ebuild
deleted file mode 100644
index 3ea8ce1..0000000
--- a/sci-biology/mira/mira-3.2.1.20.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-MIRA_3RDPARTY_PV="17-04-2010"
-
-inherit autotools base multilib
-
-DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina"
-HOMEPAGE="http://www.chevreux.org/projects_mira.html"
-SRC_URI="mirror://sourceforge/mira-assembler/${P}.tar.bz2
- mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-
-CDEPEND=">=dev-libs/boost-1.41.0-r3
- dev-util/google-perftools"
-DEPEND="${CDEPEND}
- dev-libs/expat"
-RDEPEND="${CDEPEND}
- sci-biology/smalt-bin
- sci-biology/ssaha2-bin"
-
-src_prepare() {
- find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die
- epatch "${FILESDIR}"/${PN}-3.0.0-asneeded.patch
- # http://sourceforge.net/apps/trac/mira-assembler/ticket/47
- epatch "${FILESDIR}"/mira_left_clip.readpool.C.patch
- epatch "${FILESDIR}"/libtool.m4.patch
- AT_M4DIR="config/m4" eautoreconf
- #epatch "${FILESDIR}"/libtool.patch
-}
-
-src_configure() {
- econf \
- --with-boost="${EPREFIX}"/usr/$(get_libdir) \
- --with-boost-libdir="${EPREFIX}"/usr/$(get_libdir) \
- --with-boost-thread=boost_thread-mt
-}
-
-src_compile() {
- base_src_compile
- # TODO: resolve docbook incompatibility for building docs
- if use doc; then emake -C doc clean docs || die "This will probably die because upstream did not imrove re-genartion of the docs yet."; fi
-}
-
-src_install() {
- einstall || die
- dodoc AUTHORS GETTING_STARTED NEWS README* HELP_WANTED THANKS INSTALL
- find doc/docs/man -type f | xargs doman
- find doc/docs/texinfo -type f | xargs doinfo
- dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
-}
diff --git a/sci-biology/mira/mira-3.4.0.1.ebuild b/sci-biology/mira/mira-3.4.0.1.ebuild
index 78d1cc3..45d9911 100644
--- a/sci-biology/mira/mira-3.4.0.1.ebuild
+++ b/sci-biology/mira/mira-3.4.0.1.ebuild
@@ -1,16 +1,17 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=3
+EAPI=4
MIRA_3RDPARTY_PV="09-09-2011"
-inherit autotools base multilib
+inherit autotools eutils multilib
DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina"
HOMEPAGE="http://www.chevreux.org/projects_mira.html"
-SRC_URI="mirror://sourceforge/mira-assembler/${P}.tar.bz2
+SRC_URI="
+ mirror://sourceforge/mira-assembler/${P}.tar.bz2
mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
LICENSE="GPL-2"
@@ -18,8 +19,9 @@ SLOT="0"
IUSE=""
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-CDEPEND=">=dev-libs/boost-1.41.0-r3
- dev-util/google-perftools"
+CDEPEND="
+ >=dev-libs/boost-1.41.0-r3
+ dev-util/google-perftools"
DEPEND="${CDEPEND}
dev-libs/expat"
RDEPEND="${CDEPEND}
@@ -29,8 +31,9 @@ RDEPEND="${CDEPEND}
src_prepare() {
find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die
# http://sourceforge.net/apps/trac/mira-assembler/ticket/47
- epatch "${FILESDIR}"/mira_left_clip.readpool.C.patch
- epatch "${FILESDIR}"/libtool.m4.patch
+ epatch \
+ "${FILESDIR}"/mira_left_clip.readpool.C.patch \
+ "${FILESDIR}"/libtool.m4.patch
AT_M4DIR="config/m4" eautoreconf
#epatch "${FILESDIR}"/libtool.patch
}
@@ -43,13 +46,15 @@ src_configure() {
}
src_compile() {
- base_src_compile
+ default
# TODO: resolve docbook incompatibility for building docs
- if use doc; then emake -C doc clean docs || die "This will probably die because upstream did not improve re-generation of the docs yet."; fi
+ if use doc; then
+ emake -C doc clean docs || die "This will probably die because upstream did not improve re-generation of the docs yet."
+ fi
}
src_install() {
- einstall || die
+ default
dodoc AUTHORS GETTING_STARTED NEWS README* HELP_WANTED THANKS INSTALL
find doc/docs/man -type f | xargs doman
find doc/docs/texinfo -type f | xargs doinfo
next reply other threads:[~2012-05-22 19:44 UTC|newest]
Thread overview: 12+ messages / expand[flat|nested] mbox.gz Atom feed top
2012-05-22 19:43 Justin Lecher [this message]
-- strict thread matches above, loose matches on Subject: below --
2014-04-20 0:18 [gentoo-commits] proj/sci:master commit in: sci-biology/mira/ Martin Mokrejs
2014-04-12 12:35 Martin Mokrejs
2014-01-06 17:18 Justin Lecher
2013-11-12 20:20 Martin Mokrejs
2013-10-01 13:03 Martin Mokrejs
2013-09-25 14:33 Justin Lecher
2013-09-25 13:35 Martin Mokrejs
2013-04-30 9:42 Martin Mokrejs
2011-07-05 8:22 Martin Mokrejs
2011-06-10 15:23 Martin Mokrejs
2011-05-18 16:18 Martin Mokrejs
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