* [gentoo-commits] proj/sci:master commit in: sci-biology/mira/
@ 2011-07-05 8:22 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2011-07-05 8:22 UTC (permalink / raw
To: gentoo-commits
commit: e8d6087005fecd88056d173b940a2cd39a9e0e2c
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jul 5 08:22:32 2011 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jul 5 08:22:32 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e8d60870
sci-biology/mira-3.2.1.20: version bump
(Portage version: 2.1.10.3/git/Linux i686, unsigned Manifest commit)
---
.../{mira-3.2.1.18.ebuild => mira-3.2.1.20.ebuild} | 0
1 files changed, 0 insertions(+), 0 deletions(-)
diff --git a/sci-biology/mira/mira-3.2.1.18.ebuild b/sci-biology/mira/mira-3.2.1.20.ebuild
similarity index 100%
rename from sci-biology/mira/mira-3.2.1.18.ebuild
rename to sci-biology/mira/mira-3.2.1.20.ebuild
^ permalink raw reply [flat|nested] 12+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/mira/
@ 2014-04-20 0:18 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2014-04-20 0:18 UTC (permalink / raw
To: gentoo-commits
commit: b7ea348e4b0d9a92113696cc79860bdec3e5f3ce
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr 20 00:16:46 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr 20 00:16:46 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b7ea348e
sci-biology/mira-4.0.2: version bump
Package-Manager: portage-2.2.7
---
sci-biology/mira/{mira-4.0.1.ebuild => mira-4.0.2.ebuild} | 0
1 file changed, 0 insertions(+), 0 deletions(-)
diff --git a/sci-biology/mira/mira-4.0.1.ebuild b/sci-biology/mira/mira-4.0.2.ebuild
similarity index 100%
rename from sci-biology/mira/mira-4.0.1.ebuild
rename to sci-biology/mira/mira-4.0.2.ebuild
^ permalink raw reply [flat|nested] 12+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/mira/
@ 2014-04-12 12:35 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2014-04-12 12:35 UTC (permalink / raw
To: gentoo-commits
commit: 97b1cf9bacba1cede303203987f487a1290bc60e
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Apr 12 12:28:06 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Apr 12 12:28:06 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=97b1cf9b
sci-biology/mira-4.0.1: bump to current recommended bugfix release
Package-Manager: portage-2.2.7
---
sci-biology/mira/ChangeLog | 5 +++
sci-biology/mira/mira-4.0.1.ebuild | 76 ++++++++++++++++++++++++++++++++++++++
2 files changed, 81 insertions(+)
diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog
index 4dd3e5b..b5f200e 100644
--- a/sci-biology/mira/ChangeLog
+++ b/sci-biology/mira/ChangeLog
@@ -2,6 +2,11 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*mira-4.0.1 (12 Apr 2014)
+
+ 12 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +mira-4.0.1.ebuild:
+ sci-biology/mira-4.0.1: bump to current recommended bugfix release
+
06 Jan 2014; Justin Lecher <jlec@gentoo.org> -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-4.0.1.ebuild b/sci-biology/mira/mira-4.0.1.ebuild
new file mode 100644
index 0000000..f9c38fa
--- /dev/null
+++ b/sci-biology/mira/mira-4.0.1.ebuild
@@ -0,0 +1,76 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+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}"/${PN}-3.4.0.2-boost-1.50.patch
+
+ sed \
+ -e "s:-O[23]::g" \
+ -e "s:-funroll-loops::g" \
+ -i configure.ac || die
+
+ eautoreconf
+}
+
+src_configure() {
+ econf \
+ --with-boost="${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"
+}
^ permalink raw reply related [flat|nested] 12+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/mira/
@ 2014-01-06 17:18 Justin Lecher
0 siblings, 0 replies; 12+ messages in thread
From: Justin Lecher @ 2014-01-06 17:18 UTC (permalink / raw
To: gentoo-commits
commit: 1be11cbcf6ff6f592b5e652694394899dbe2ae0f
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 6 15:56:39 2014 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> 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 <jlec@gentoo.org> -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 <mmokrejs@fold.natur.cuni.cz>
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"
^ permalink raw reply related [flat|nested] 12+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/mira/
@ 2013-11-12 20:20 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2013-11-12 20:20 UTC (permalink / raw
To: gentoo-commits
commit: ddb381cc314cdb15f745533a8a0cb379b856a120
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Nov 12 20:19:45 2013 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Nov 12 20:19:45 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ddb381cc
sci-biology/mira-4.0_rc4: Added 4.0_rc4 release candidate. Removing the sed hack redirecting autoconf to config/m4/ instead of m4/ because upstream accepted that source tree layout change in _rc3 already.
Package-Manager: portage-2.2.7
---
sci-biology/mira/ChangeLog | 8 ++++
sci-biology/mira/mira-3.4.0.1.ebuild | 2 +-
sci-biology/mira/mira-4.0_rc4.ebuild | 76 ++++++++++++++++++++++++++++++++++++
3 files changed, 85 insertions(+), 1 deletion(-)
diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog
index 7ea6f3b..56cb51d 100644
--- a/sci-biology/mira/ChangeLog
+++ b/sci-biology/mira/ChangeLog
@@ -2,6 +2,14 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 12 Nov 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ 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:
+ Added 4.0_rc4 release candidate. Removing the sed hack redirecting autoconf
+ to config/m4/ instead of m4/ because upstream accepted that source tree
+ layout change in _rc3 already.
+
+
01 Oct 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
mira-4.0_rc2.ebuild:
Improve ebuild to use MY_PV.
diff --git a/sci-biology/mira/mira-3.4.0.1.ebuild b/sci-biology/mira/mira-3.4.0.1.ebuild
index 45d9911..88d150a 100644
--- a/sci-biology/mira/mira-3.4.0.1.ebuild
+++ b/sci-biology/mira/mira-3.4.0.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
diff --git a/sci-biology/mira/mira-4.0_rc4.ebuild b/sci-biology/mira/mira-4.0_rc4.ebuild
new file mode 100644
index 0000000..813eee0
--- /dev/null
+++ b/sci-biology/mira/mira-4.0_rc4.ebuild
@@ -0,0 +1,76 @@
+# 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}"/${PN}-3.4.0.2-boost-1.50.patch
+
+ sed \
+ -e "s:-O[23]::g" \
+ -e "s:-funroll-loops::g" \
+ -i configure.ac || die
+
+ eautoreconf
+}
+
+src_configure() {
+ econf \
+ --with-boost="${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"
+}
^ permalink raw reply related [flat|nested] 12+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/mira/
@ 2013-10-01 13:03 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2013-10-01 13:03 UTC (permalink / raw
To: gentoo-commits
commit: bda8fb1dc8bcbe8b80ec358e178a3c66ac7547a0
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Oct 1 13:02:40 2013 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Oct 1 13:02:40 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bda8fb1d
Improve ebuild to use MY_PV
Package-Manager: portage-2.1.12.2
---
sci-biology/mira/ChangeLog | 4 ++++
sci-biology/mira/mira-4.0_rc2.ebuild | 6 ++++--
2 files changed, 8 insertions(+), 2 deletions(-)
diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog
index bd72985..7ea6f3b 100644
--- a/sci-biology/mira/ChangeLog
+++ b/sci-biology/mira/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 01 Oct 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ mira-4.0_rc2.ebuild:
+ Improve ebuild to use MY_PV.
+
25 Sep 2013; Justin Lecher <jlec@gentoo.org> mira-4.0_rc2.ebuild,
metadata.xml:
Fix m4 macrodir location
diff --git a/sci-biology/mira/mira-4.0_rc2.ebuild b/sci-biology/mira/mira-4.0_rc2.ebuild
index 48a135a..2c26f0a 100644
--- a/sci-biology/mira/mira-4.0_rc2.ebuild
+++ b/sci-biology/mira/mira-4.0_rc2.ebuild
@@ -5,17 +5,19 @@
EAPI=5
MIRA_3RDPARTY_PV="06-07-2012"
+MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived) to mira-4.0rc2 (upstream fromat)
+
inherit autotools eutils multilib
DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina"
HOMEPAGE="http://www.chevreux.org/projects_mira.html"
-SRC_URI="http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/mira-4.0rc2.tar.bz2
+SRC_URI="http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${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"
-S="${WORKDIR}/mira-4.0rc2"
+S="${WORKDIR}"/"${PN}"-"${MY_PV}"
SLOT="0"
LICENSE="GPL-2"
^ permalink raw reply related [flat|nested] 12+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/mira/
@ 2013-09-25 14:33 Justin Lecher
0 siblings, 0 replies; 12+ messages in thread
From: Justin Lecher @ 2013-09-25 14:33 UTC (permalink / raw
To: gentoo-commits
commit: f27a3ee1061d4a2aa0d81db7863700d6a49cd507
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Sep 25 14:32:27 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Sep 25 14:32:27 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f27a3ee1
sci-biology/mira: Fix m4 macrodir location
Package-Manager: portage-2.2.7
---
sci-biology/mira/ChangeLog | 4 ++++
sci-biology/mira/metadata.xml | 10 +++++-----
sci-biology/mira/mira-4.0_rc2.ebuild | 8 +++++---
3 files changed, 14 insertions(+), 8 deletions(-)
diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog
index afda6bd..bd72985 100644
--- a/sci-biology/mira/ChangeLog
+++ b/sci-biology/mira/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 25 Sep 2013; Justin Lecher <jlec@gentoo.org> mira-4.0_rc2.ebuild,
+ metadata.xml:
+ Fix m4 macrodir location
+
*mira-3.9.15 (30 Apr 2013)
30 Apr 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/mira/metadata.xml b/sci-biology/mira/metadata.xml
index 07b5255..2bc8930 100644
--- a/sci-biology/mira/metadata.xml
+++ b/sci-biology/mira/metadata.xml
@@ -1,9 +1,9 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <herd>sci-biology</herd>
- <maintainer>
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
</pkgmetadata>
diff --git a/sci-biology/mira/mira-4.0_rc2.ebuild b/sci-biology/mira/mira-4.0_rc2.ebuild
index 13df7b7..48a135a 100644
--- a/sci-biology/mira/mira-4.0_rc2.ebuild
+++ b/sci-biology/mira/mira-4.0_rc2.ebuild
@@ -44,9 +44,11 @@ src_prepare() {
-e "s:-funroll-loops::g" \
-i configure.ac || die
- ln -s config/m4 .
- AT_M4DIR="config/m4" eaclocal
- AT_M4DIR="config/m4" eautoreconf
+ sed \
+ -e 's:m4:config/m4:g' \
+ -i Makefile.am configure.ac || die
+
+ eautoreconf
}
src_configure() {
^ permalink raw reply related [flat|nested] 12+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/mira/
@ 2013-09-25 13:35 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2013-09-25 13:35 UTC (permalink / raw
To: gentoo-commits
commit: bc1bf424a20c10b9a2ae6e2bfd337d47173e3810
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Sep 25 13:36:49 2013 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Sep 25 13:36:49 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bc1bf424
version bump
---
sci-biology/mira/mira-4.0_rc2.ebuild | 76 ++++++++++++++++++++++++++++++++++++
1 file changed, 76 insertions(+)
diff --git a/sci-biology/mira/mira-4.0_rc2.ebuild b/sci-biology/mira/mira-4.0_rc2.ebuild
new file mode 100644
index 0000000..13df7b7
--- /dev/null
+++ b/sci-biology/mira/mira-4.0_rc2.ebuild
@@ -0,0 +1,76 @@
+# 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"
+
+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/mira-4.0rc2.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}/mira-4.0rc2"
+
+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
+
+ ln -s config/m4 .
+ AT_M4DIR="config/m4" eaclocal
+ 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() {
+ 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"
+}
^ permalink raw reply related [flat|nested] 12+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/mira/
@ 2013-04-30 9:42 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2013-04-30 9:42 UTC (permalink / raw
To: gentoo-commits
commit: 00bb77fe4833272c18c448942d8e19b99d729e77
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Apr 30 09:42:18 2013 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Apr 30 09:42:18 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=00bb77fe
sci-biology/mira-3.9.15: bump to current besta version
Package-Manager: portage-2.1.11.62
---
sci-biology/mira/ChangeLog | 6 +++
sci-biology/mira/mira-3.9.15.ebuild | 64 +++++++++++++++++++++++++++++++++++
2 files changed, 70 insertions(+), 0 deletions(-)
diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog
index 68b66f6..afda6bd 100644
--- a/sci-biology/mira/ChangeLog
+++ b/sci-biology/mira/ChangeLog
@@ -2,6 +2,12 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*mira-3.9.15 (30 Apr 2013)
+
+ 30 Apr 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +mira-3.9.15.ebuild:
+ sci-biology/mira-3.9.15: bump to current besta version mira-3.9.15.ebuild
+
*mira-3.4.1.1 (22 Feb 2013)
*mira-3.9.9 (22 Feb 2013)
diff --git a/sci-biology/mira/mira-3.9.15.ebuild b/sci-biology/mira/mira-3.9.15.ebuild
new file mode 100644
index 0000000..8dbb921
--- /dev/null
+++ b/sci-biology/mira/mira-3.9.15.ebuild
@@ -0,0 +1,64 @@
+# 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"
+}
^ permalink raw reply related [flat|nested] 12+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/mira/
@ 2012-05-22 19:43 Justin Lecher
0 siblings, 0 replies; 12+ messages in thread
From: Justin Lecher @ 2012-05-22 19:43 UTC (permalink / raw
To: gentoo-commits
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
^ permalink raw reply related [flat|nested] 12+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/mira/
@ 2011-06-10 15:23 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2011-06-10 15:23 UTC (permalink / raw
To: gentoo-commits
commit: 4d513f25a4f25b460f1d396543851760bbc54bcf
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon May 23 12:59:22 2011 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon May 23 12:59:22 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4d513f25
sci-biology/mira: revbump to force inclusion on dev-util/google-perftools deps
(Portage version: 2.1.9.49/git/Linux i686, unsigned Manifest commit)
---
.../{mira-3.2.1-r1.ebuild => mira-3.2.1-r2.ebuild} | 3 ++-
sci-biology/mira/mira-3.2.1.17-r1.ebuild | 5 +++--
2 files changed, 5 insertions(+), 3 deletions(-)
diff --git a/sci-biology/mira/mira-3.2.1-r1.ebuild b/sci-biology/mira/mira-3.2.1-r2.ebuild
similarity index 96%
rename from sci-biology/mira/mira-3.2.1-r1.ebuild
rename to sci-biology/mira/mira-3.2.1-r2.ebuild
index 020876c..a4de8cc 100644
--- a/sci-biology/mira/mira-3.2.1-r1.ebuild
+++ b/sci-biology/mira/mira-3.2.1-r2.ebuild
@@ -18,7 +18,8 @@ SLOT="0"
IUSE=""
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-CDEPEND=">=dev-libs/boost-1.41.0-r3"
+CDEPEND=">=dev-libs/boost-1.41.0-r3
+ dev-util/google-perftools"
DEPEND="${CDEPEND}
dev-libs/expat"
RDEPEND="${CDEPEND}
diff --git a/sci-biology/mira/mira-3.2.1.17-r1.ebuild b/sci-biology/mira/mira-3.2.1.17-r1.ebuild
index 49e97f6..9fe96ff 100644
--- a/sci-biology/mira/mira-3.2.1.17-r1.ebuild
+++ b/sci-biology/mira/mira-3.2.1.17-r1.ebuild
@@ -20,7 +20,8 @@ KEYWORDS=""
# masked because of 'libtool: Version mismatch error. This is libtool 2.4, but the definition of this LT_INIT comes from libtool 2.2.6b. You should recreate aclocal.m4 with macros from libtool 2.4 and run autoconf again.', dyeing at src/examples_programming/
#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-CDEPEND=">=dev-libs/boost-1.41.0-r3"
+CDEPEND=">=dev-libs/boost-1.41.0-r3
+ dev-util/google-perftools"
DEPEND="${CDEPEND}
dev-libs/expat"
RDEPEND="${CDEPEND}
@@ -45,7 +46,7 @@ src_configure() {
src_compile() {
base_src_compile
# TODO: resolve docbook incompatibility for building docs
- if use doc; then emake -C doc clean docs || die; fi
+ if use doc; then emake -C doc clean docs || die "This will probably die because upstream did not imrove re-genartion of the docs yet."; fi
}
src_install() {
^ permalink raw reply related [flat|nested] 12+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/mira/
@ 2011-05-18 16:18 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2011-05-18 16:18 UTC (permalink / raw
To: gentoo-commits
commit: 3751e59f2601bea758e63a00485a64d3edeec1a1
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed May 18 16:17:52 2011 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed May 18 16:17:52 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3751e59f
sci-biology/mira-3.2.1.17-r1: maks the devel. version until it can be compiled (due autoreconf issues)
(Portage version: 2.1.9.43/git/Linux i686, unsigned Manifest commit)
---
sci-biology/mira/mira-3.2.1.17-r1.ebuild | 4 +++-
1 files changed, 3 insertions(+), 1 deletions(-)
diff --git a/sci-biology/mira/mira-3.2.1.17-r1.ebuild b/sci-biology/mira/mira-3.2.1.17-r1.ebuild
index 020876c..49e97f6 100644
--- a/sci-biology/mira/mira-3.2.1.17-r1.ebuild
+++ b/sci-biology/mira/mira-3.2.1.17-r1.ebuild
@@ -16,7 +16,9 @@ SRC_URI="mirror://sourceforge/mira-assembler/${P}.tar.bz2
LICENSE="GPL-2"
SLOT="0"
IUSE=""
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
+KEYWORDS=""
+# masked because of 'libtool: Version mismatch error. This is libtool 2.4, but the definition of this LT_INIT comes from libtool 2.2.6b. You should recreate aclocal.m4 with macros from libtool 2.4 and run autoconf again.', dyeing at src/examples_programming/
+#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
CDEPEND=">=dev-libs/boost-1.41.0-r3"
DEPEND="${CDEPEND}
^ permalink raw reply related [flat|nested] 12+ messages in thread
end of thread, other threads:[~2014-04-20 0:19 UTC | newest]
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