sci-biology/mira: Version Bump, #377807

(Portage version: 2.2.0_alpha142/cvs/Linux x86_64, signed Manifest commit with key 8009D6F070EB7916)

5 files changed, 97 insertions, 5 deletions

diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog
index deab5fc1068a..93cb6f858459 100644
--- a/sci-biology/mira/ChangeLog
+++ b/sci-biology/mira/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/mira
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/ChangeLog,v 1.19 2012/11/07 22:10:54 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/ChangeLog,v 1.20 2012/11/07 22:29:55 jlec Exp $
+
+*mira-3.4.0.2 (07 Nov 2012)
+
+  07 Nov 2012; Justin Lecher <jlec@gentoo.org> mira-3.2.1.ebuild,
+  mira-3.2.1-r1.ebuild, +mira-3.4.0.2.ebuild,
+  +files/mira-3.4.0.2-boost-1.50.patch:
+  Version Bump, #377807
 
 *mira-3.2.1-r1 (07 Nov 2012)
 
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 000000000000..427192294c81
--- /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-3.2.1-r1.ebuild b/sci-biology/mira/mira-3.2.1-r1.ebuild
index c6bddae49f03..b4d434df4a9b 100644
--- a/sci-biology/mira/mira-3.2.1-r1.ebuild
+++ b/sci-biology/mira/mira-3.2.1-r1.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-3.2.1-r1.ebuild,v 1.1 2012/11/07 22:10:54 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-3.2.1-r1.ebuild,v 1.2 2012/11/07 22:29:55 jlec Exp $
 
 EAPI=4
 
@@ -16,8 +16,8 @@ SRC_URI="
 
 SLOT="0"
 LICENSE="GPL-2"
-IUSE=""
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
+IUSE=""
 
 CDEPEND="
 	dev-libs/boost
diff --git a/sci-biology/mira/mira-3.2.1.ebuild b/sci-biology/mira/mira-3.2.1.ebuild
index 097615084e00..658a361a1112 100644
--- a/sci-biology/mira/mira-3.2.1.ebuild
+++ b/sci-biology/mira/mira-3.2.1.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-3.2.1.ebuild,v 1.6 2012/11/07 22:10:54 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-3.2.1.ebuild,v 1.7 2012/11/07 22:29:55 jlec Exp $
 
 EAPI="3"
 
@@ -16,8 +16,8 @@ SRC_URI="
 
 SLOT="0"
 LICENSE="GPL-2"
-IUSE=""
 KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~x86-macos"
+IUSE=""
 
 CDEPEND="
 	dev-libs/boost
diff --git a/sci-biology/mira/mira-3.4.0.2.ebuild b/sci-biology/mira/mira-3.4.0.2.ebuild
new file mode 100644
index 000000000000..e3582fddd25c
--- /dev/null
+++ b/sci-biology/mira/mira-3.4.0.2.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2012 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="
+	mirror://sourceforge/mira-assembler/${P}.tar.bz2
+	mirror://sourceforge/mira-assembler/mira_3rdparty_${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 \
+		"${FILESDIR}"/${P}-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"
+}