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Mon, 6 Jan 2014 17:18:32 +0000 (UTC) From: "Justin Lecher" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Justin Lecher" Message-ID: <1389023799.1be11cbcf6ff6f592b5e652694394899dbe2ae0f.jlec@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/mira/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/mira/ChangeLog sci-biology/mira/mira-3.4.0.1.ebuild sci-biology/mira/mira-3.4.1.1.ebuild sci-biology/mira/mira-3.9.15.ebuild sci-biology/mira/mira-3.9.9.ebuild sci-biology/mira/mira-4.0_rc2.ebuild sci-biology/mira/mira-4.0_rc4.ebuild X-VCS-Directories: sci-biology/mira/ X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: 1be11cbcf6ff6f592b5e652694394899dbe2ae0f X-VCS-Branch: master Date: Mon, 6 Jan 2014 17:18:32 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: 1990a316-69d3-4372-b4ef-2fcd6c7996af X-Archives-Hash: 99aa09a594332fee17084f7c9b299c4d commit: 1be11cbcf6ff6f592b5e652694394899dbe2ae0f Author: Justin Lecher gentoo org> AuthorDate: Mon Jan 6 15:56:39 2014 +0000 Commit: Justin Lecher gentoo org> CommitDate: Mon Jan 6 15:56:39 2014 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1be11cbc sci-biology/mira: Drop old; punt base.eclass Package-Manager: portage-2.2.8 --- sci-biology/mira/ChangeLog | 7 +++- sci-biology/mira/mira-3.4.0.1.ebuild | 62 ---------------------------- sci-biology/mira/mira-3.4.1.1.ebuild | 61 --------------------------- sci-biology/mira/mira-3.9.15.ebuild | 64 ----------------------------- sci-biology/mira/mira-3.9.9.ebuild | 61 --------------------------- sci-biology/mira/mira-4.0_rc2.ebuild | 80 ------------------------------------ sci-biology/mira/mira-4.0_rc4.ebuild | 6 +-- 7 files changed, 9 insertions(+), 332 deletions(-) diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog index 56cb51d..4dd3e5b 100644 --- a/sci-biology/mira/ChangeLog +++ b/sci-biology/mira/ChangeLog @@ -1,7 +1,12 @@ # ChangeLog for sci-biology/mira -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jan 2014; Justin Lecher -mira-3.4.0.1.ebuild, + -mira-3.4.1.1.ebuild, -mira-3.9.9.ebuild, -mira-3.9.15.ebuild, + -mira-4.0_rc2.ebuild, mira-4.0_rc4.ebuild: + Drop old; punt base.eclass + 12 Nov 2013; Martin Mokrejs mira-3.4.0.1.ebuild, mira-3.4.1.1.ebuild, mira-3.9.9.ebuild, mira-3.9.15.ebuild, mira-4.0_rc2.ebuild, +mira-4.0_rc4.ebuild: diff --git a/sci-biology/mira/mira-3.4.0.1.ebuild b/sci-biology/mira/mira-3.4.0.1.ebuild deleted file mode 100644 index 88d150a..0000000 --- a/sci-biology/mira/mira-3.4.0.1.ebuild +++ /dev/null @@ -1,62 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=4 - -MIRA_3RDPARTY_PV="09-09-2011" - -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/${P}.tar.bz2 - mirror://sourceforge/mira-assembler/mira_3rdparty_${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 - # http://sourceforge.net/apps/trac/mira-assembler/ticket/47 - epatch \ - "${FILESDIR}"/mira_left_clip.readpool.C.patch \ - "${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/$(get_libdir) \ - --with-boost-thread=boost_thread-mt -} - -src_compile() { - default - # TODO: resolve docbook incompatibility for building docs - if use doc; then - emake -C doc clean docs || die "This will probably die because upstream did not improve re-generation of the docs yet." - fi -} - -src_install() { - default - dodoc AUTHORS GETTING_STARTED NEWS README* HELP_WANTED THANKS INSTALL - find doc/docs/man -type f | xargs doman - find doc/docs/texinfo -type f | xargs doinfo - dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl} -} diff --git a/sci-biology/mira/mira-3.4.1.1.ebuild b/sci-biology/mira/mira-3.4.1.1.ebuild deleted file mode 100644 index 5260ee1..0000000 --- a/sci-biology/mira/mira-3.4.1.1.ebuild +++ /dev/null @@ -1,61 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-3.4.0.2.ebuild,v 1.1 2012/11/07 22:29:56 jlec Exp $ - -EAPI=4 - -MIRA_3RDPARTY_PV="06-07-2012" - -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=" - http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/${P}.tar.gz - mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" - -SLOT="0" -LICENSE="GPL-2" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos" -IUSE="" - -CDEPEND=" - dev-libs/boost - dev-util/google-perftools" -DEPEND="${CDEPEND} - app-editors/vim-core - dev-libs/expat" -RDEPEND="${CDEPEND}" - -DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED - THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf ) - -src_prepare() { - find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die - epatch \ - "${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.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() { - base_src_install - dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl} -} - -pkg_postinst() { - einfo "Documentation is no longer built, you can find it at:" - einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html" -} diff --git a/sci-biology/mira/mira-3.9.15.ebuild b/sci-biology/mira/mira-3.9.15.ebuild deleted file mode 100644 index 8dbb921..0000000 --- a/sci-biology/mira/mira-3.9.15.ebuild +++ /dev/null @@ -1,64 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-3.4.0.2.ebuild,v 1.1 2012/11/07 22:29:56 jlec Exp $ - -EAPI=4 - -MIRA_3RDPARTY_PV="06-07-2012" - -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=" - http://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2 - mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" - -SLOT="0" -LICENSE="GPL-2" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos" -IUSE="doc" - -CDEPEND=" - dev-libs/boost - dev-util/google-perftools" -DEPEND="${CDEPEND} - app-editors/vim-core - dev-libs/expat" -RDEPEND="${CDEPEND}" - -#DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED -# THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf ) -DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED - THANKS ) - -src_prepare() { - find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die - epatch \ - "${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.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() { - base_src_install - dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl} - dodoc "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta} -} - -pkg_postinst() { - einfo "Documentation is no longer built, you can find it at:" - einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html" -} diff --git a/sci-biology/mira/mira-3.9.9.ebuild b/sci-biology/mira/mira-3.9.9.ebuild deleted file mode 100644 index 0deeb87..0000000 --- a/sci-biology/mira/mira-3.9.9.ebuild +++ /dev/null @@ -1,61 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-3.4.0.2.ebuild,v 1.1 2012/11/07 22:29:56 jlec Exp $ - -EAPI=4 - -MIRA_3RDPARTY_PV="06-07-2012" - -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=" - http://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2 - mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" - -SLOT="0" -LICENSE="GPL-2" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos" -IUSE="" - -CDEPEND=" - dev-libs/boost - dev-util/google-perftools" -DEPEND="${CDEPEND} - app-editors/vim-core - dev-libs/expat" -RDEPEND="${CDEPEND}" - -DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED - THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf ) - -src_prepare() { - find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die - epatch \ - "${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.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() { - base_src_install - dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl} -} - -pkg_postinst() { - einfo "Documentation is no longer built, you can find it at:" - einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html" -} diff --git a/sci-biology/mira/mira-4.0_rc2.ebuild b/sci-biology/mira/mira-4.0_rc2.ebuild deleted file mode 100644 index 2c26f0a..0000000 --- a/sci-biology/mira/mira-4.0_rc2.ebuild +++ /dev/null @@ -1,80 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-3.9.18.ebuild,v 1.1 2013/07/07 19:41:05 jlec Exp $ - -EAPI=5 - -MIRA_3RDPARTY_PV="06-07-2012" -MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived) to mira-4.0rc2 (upstream fromat) - - -inherit autotools eutils multilib - -DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina" -HOMEPAGE="http://www.chevreux.org/projects_mira.html" -SRC_URI="http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${PN}"-"${MY_PV}".tar.bz2 - mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" -# http://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2 -# mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" - -S="${WORKDIR}"/"${PN}"-"${MY_PV}" - -SLOT="0" -LICENSE="GPL-2" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos" -IUSE="doc" - -CDEPEND=" - dev-libs/boost - dev-util/google-perftools" -DEPEND="${CDEPEND} - app-editors/vim-core - dev-libs/expat" -RDEPEND="${CDEPEND}" - -#DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED -# THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf ) -DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED THANKS ) - -src_prepare() { - find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die - epatch \ - "${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.patch - - sed \ - -e "s:-O[23]::g" \ - -e "s:-funroll-loops::g" \ - -i configure.ac || die - - sed \ - -e 's:m4:config/m4:g' \ - -i Makefile.am configure.ac || die - - eautoreconf -} - -src_configure() { - econf \ - --with-boost="${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() { - default - dodoc ${DOCS[@]} - - dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl} - dodoc "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta} -} - -pkg_postinst() { - einfo "Documentation is no longer built, you can find it at:" - einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html" -} diff --git a/sci-biology/mira/mira-4.0_rc4.ebuild b/sci-biology/mira/mira-4.0_rc4.ebuild index 813eee0..682bf23 100644 --- a/sci-biology/mira/mira-4.0_rc4.ebuild +++ b/sci-biology/mira/mira-4.0_rc4.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2013 Gentoo Foundation +# Copyright 1999-2014 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-3.9.18.ebuild,v 1.1 2013/07/07 19:41:05 jlec Exp $ @@ -7,12 +7,12 @@ EAPI=5 MIRA_3RDPARTY_PV="06-07-2012" MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived) to mira-4.0rc2 (upstream fromat) - inherit autotools eutils multilib DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina" HOMEPAGE="http://www.chevreux.org/projects_mira.html" -SRC_URI="http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${PN}"-"${MY_PV}".tar.bz2 +SRC_URI=" + http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${PN}"-"${MY_PV}".tar.bz2 mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" # http://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2 # mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"