diff options
-rw-r--r-- | sci-biology/mira/ChangeLog | 7 | ||||
-rw-r--r-- | sci-biology/mira/Manifest | 4 | ||||
-rw-r--r-- | sci-biology/mira/mira-3.2.1-r2.ebuild | 57 | ||||
-rw-r--r-- | sci-biology/mira/mira-3.2.1.17-r1.ebuild | 57 | ||||
-rw-r--r-- | sci-biology/mira/mira-3.2.1.20.ebuild | 58 | ||||
-rw-r--r-- | sci-biology/mira/mira-3.4.0.1.ebuild | 27 |
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 |