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-rw-r--r--sci-biology/mira/ChangeLog7
-rw-r--r--sci-biology/mira/Manifest4
-rw-r--r--sci-biology/mira/mira-3.2.1-r2.ebuild57
-rw-r--r--sci-biology/mira/mira-3.2.1.17-r1.ebuild57
-rw-r--r--sci-biology/mira/mira-3.2.1.20.ebuild58
-rw-r--r--sci-biology/mira/mira-3.4.0.1.ebuild27
6 files changed, 22 insertions, 188 deletions
diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog
index 0982f998f..4cd234f7e 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/Manifest b/sci-biology/mira/Manifest
index 4ae708ab5..2bebb9aa7 100644
--- a/sci-biology/mira/Manifest
+++ b/sci-biology/mira/Manifest
@@ -1,6 +1,2 @@
-DIST mira-3.2.1.17.tar.bz2 9611305 RMD160 b9a124c572763fa8923c1b1ee5b12e54b881b67c SHA1 a2731ba4da5af9f0c575ff355a481ea0190dd898 SHA256 2d79ebbbfc6801ff500cabd79cd63358e50296fbdcd1aed4028ea52503d76f8c
-DIST mira-3.2.1.20.tar.bz2 9619538 RMD160 9838827d50b7ee2a726be4ee3badec25bd5c5799 SHA1 73fd04dffb3e3a7bb5425b16e565f5e85584e215 SHA256 38eb701b6585696a70b7ad8aae7285059415c7b335c9138c014002d2a8289a83
-DIST mira-3.2.1.tar.bz2 9626154 RMD160 b998226fe4ea0efbe6023dac8b073af1782167b9 SHA1 432d1ecd2acb62a8584f29a10b55943165cd0586 SHA256 86a2c00d182573008ef41f7725aec72ea69756ea9f3dc7e798a7d253a47f8bd7
DIST mira-3.4.0.1.tar.bz2 10262667 RMD160 dc008eeb8dd291f9255f7b50ec5e0f888004cddd SHA1 a993c4e30d85b063768d3c5c1af7c3a5d5ff2aa4 SHA256 cafe45601b3c143ac142c022e1fc0a21544e880bb226897824de5dbf6d516d7e
DIST mira_3rdparty_09-09-2011.tar.bz2 31285 RMD160 9c890ed445b75c2caf46c91adfb7040e7e9309c1 SHA1 c650b903861218854b8976bf3ebe977ec06afe99 SHA256 0e00cd0efff5601d559ee8d40d29b8d3b87db3f4cd5b7bfa5970501ea43f840b
-DIST mira_3rdparty_17-04-2010.tar.bz2 31296 RMD160 888a38f865963b3109d3a331604e079010b55d81 SHA1 5f2fbe3e2e1bb5c5de44d414963e57b8dbcf760c SHA256 ec2c77508d75b7c28d3d26137ab69648b1ed653af93d486245ad0e4624e332b2
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 c110959eb..000000000
--- 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 04b37674c..000000000
--- 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 3ea8ce177..000000000
--- 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 78d1cc367..45d9911fb 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