[gentoo-commits] proj/sci:master commit in: sci-biology/mira/, sci-biology/mira/files/

["Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>]

commit:     c2386356030a1cee494636d114a52a59714fb10c
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Feb 22 00:36:44 2013 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> 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 <mmokrejs@fold.natur.cuni.cz>
+  +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 <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
@@ -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"
+}