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Fri, 22 Feb 2013 00:37:08 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <1361493404.c2386356030a1cee494636d114a52a59714fb10c.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/mira/, sci-biology/mira/files/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/mira/ChangeLog sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch sci-biology/mira/mira-3.4.1.1.ebuild sci-biology/mira/mira-3.9.9.ebuild X-VCS-Directories: sci-biology/mira/ sci-biology/mira/files/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: c2386356030a1cee494636d114a52a59714fb10c X-VCS-Branch: master Date: Fri, 22 Feb 2013 00:37:08 +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: df95ee4a-51f3-4ab3-b9bb-ffcd2bedae9d X-Archives-Hash: 21b448a57defadb0118647ea1b12f295 commit: c2386356030a1cee494636d114a52a59714fb10c Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Fri Feb 22 00:36:44 2013 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Fri Feb 22 00:36:44 2013 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c2386356 sci-biology/mira: current stable and development version bumps Package-Manager: portage-2.1.11.38 --- sci-biology/mira/ChangeLog | 11 +++- .../mira/files/mira-3.4.0.2-boost-1.50.patch | 24 ++++++++ sci-biology/mira/mira-3.4.1.1.ebuild | 61 ++++++++++++++++++++ sci-biology/mira/mira-3.9.9.ebuild | 61 ++++++++++++++++++++ 4 files changed, 155 insertions(+), 2 deletions(-) diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog index 4cd234f..68b66f6 100644 --- a/sci-biology/mira/ChangeLog +++ b/sci-biology/mira/ChangeLog @@ -1,7 +1,15 @@ # ChangeLog for sci-biology/mira -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*mira-3.4.1.1 (22 Feb 2013) +*mira-3.9.9 (22 Feb 2013) + + 22 Feb 2013; Martin Mokrejs + +files/mira-3.4.0.2-boost-1.50.patch, +mira-3.4.1.1.ebuild, + +mira-3.9.9.ebuild: + sci-biology/mira: current stable and development version bumps + 22 May 2012; Justin Lecher -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 @@ -15,4 +23,3 @@ fixed that in a different way, the still applicable part of the patch is however provided under files/ but is just a cosmetic change (hence not really needed) - diff --git a/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch b/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch new file mode 100644 index 0000000..4271922 --- /dev/null +++ b/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch @@ -0,0 +1,24 @@ + config/m4/ax_boost_regex.m4 | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/config/m4/ax_boost_regex.m4 b/config/m4/ax_boost_regex.m4 +index 1ac06af..5b7be93 100644 +--- a/config/m4/ax_boost_regex.m4 ++++ b/config/m4/ax_boost_regex.m4 +@@ -78,14 +78,14 @@ AC_DEFUN([AX_BOOST_REGEX], + for libextension in `ls $BOOSTLIBDIR/libboost_regex*.so* $BOOSTLIBDIR/libboost_regex*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_regex.*\)\.so.*$;\1;' -e 's;^lib\(boost_regex.*\)\.a*$;\1;'` ; do + ax_lib=${libextension} + AC_CHECK_LIB($ax_lib, exit, +- [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break], ++ [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break], + [link_regex="no"]) + done + if test "x$link_regex" != "xyes"; then + for libextension in `ls $BOOSTLIBDIR/boost_regex*.{dll,a}* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_regex.*\)\.dll.*$;\1;' -e 's;^\(boost_regex.*\)\.a*$;\1;'` ; do + ax_lib=${libextension} + AC_CHECK_LIB($ax_lib, exit, +- [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break], ++ [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break], + [link_regex="no"]) + done + fi diff --git a/sci-biology/mira/mira-3.4.1.1.ebuild b/sci-biology/mira/mira-3.4.1.1.ebuild new file mode 100644 index 0000000..5260ee1 --- /dev/null +++ b/sci-biology/mira/mira-3.4.1.1.ebuild @@ -0,0 +1,61 @@ +# 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-3.9.9.ebuild b/sci-biology/mira/mira-3.9.9.ebuild new file mode 100644 index 0000000..0deeb87 --- /dev/null +++ b/sci-biology/mira/mira-3.9.9.ebuild @@ -0,0 +1,61 @@ +# 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" +}