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

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

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"
+}