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

4 files changed, 86 insertions, 1 deletions

diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog
index 7ea6f3bd8..56cb51d4c 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/Manifest b/sci-biology/mira/Manifest
index 4d5034710..3fb13f0d8 100644
--- a/sci-biology/mira/Manifest
+++ b/sci-biology/mira/Manifest
@@ -3,5 +3,6 @@ DIST mira-3.4.1.1.tar.gz 11665587 SHA256 d523a75ea499886564c2f698397c21d49e970e3
 DIST mira-3.9.15.tar.bz2 10356048 SHA256 b52adf2884900f5228f2dc8540ba3cf7b85d9db3d4abbb325491696648a60a97 SHA512 4dfa3d03dbfbe97b490aeae2cdb32df7468f97dfa38bd738ca5930826c962f7444f676febb266b841e3cfc993062f793c0d9d8c6a7676d30c2df36a7f5ee017c WHIRLPOOL df6132174aedabf8ff376447277e383dff0cf263c6812a80881733664b71edb4079f9a9e7e5285a16dbf46ed721cfb3dd6e599a6caf130a6205d6a54dc67afbb
 DIST mira-3.9.9.tar.bz2 10356020 SHA256 d80929a9e7807bd0c160301c26d12b94fffd6439f8fea178b550c189da28848b SHA512 da2de917e99ac3825ac45ace7ae72b85d352eb75195db9f87679b45b3fe1a284aa6d53f5c6f3d45e1caa95e0dba20cf7a979bd97df67b65239f0aeb6e8af80d8 WHIRLPOOL 9d3a7b4e78e26b0eeb0f2e3cec804c0a99b9dbe260796f783214cf0c6b71da40fb5fd5480a4ec730e3bd3b0566b53f6e61ae1badee63460bfb4ceef006ac461c
 DIST mira-4.0rc2.tar.bz2 10389866 SHA256 7994d208898c9fb4a8779ec0ce27e6b8fd7235cf684557b07967041c710f26dd SHA512 72fb587e071a03a315b80dc8e9171f8d8d62bcc625ffc5c58264bda0135d914902c3387528c9e2405c42f61d9d367697272099a9bd41481ef9843a676232c390 WHIRLPOOL 70c5778974123cca6cd0b1515f206aa3f92ebd39f13020a2ebf3c4653ba9094afb688d827ee6d6c5c003c5ac56721eee583dc5b27f1f56d7633e79a1d98e0791
+DIST mira-4.0rc4.tar.bz2 10418692 SHA256 5149e25462625be98a18945921e17bb3c9bef110d820af295c7473a44acf09b4 SHA512 9ada6abaf36993e8738cd8fbe7ec710e0672335afc83902fd962fe9c0c430dae80df64f272bfbb1b4d132cb080e93ed791eaf8a7652b22e5e6e816466fe3eb5b WHIRLPOOL f2d605f2ad7985f60038ed93d4c1d45b6b60c97552588ac1daae449f8ee503691c0ef79d52df75bd9241cdc888a107df2801d31c9e6c9b8e3c6f3c561910c09f
 DIST mira_3rdparty_06-07-2012.tar.bz2 31656 SHA256 53cbbb9d57e2fa51706b3f1d055621c0863091542b8851f3ce8a45850951d7d2 SHA512 4d4dbdf7ab5126f9d47160bee8bc127b6a225de8087f6b9914c754324a74d966333207c86a3f38cf0ea9f91408707e2a24086dbe1318fdfa2870b0c39bc5033b WHIRLPOOL c9946ddc032d6864a33e7a60a4d1a515262ca2204535c7d81dcc73144b4f471f766007082d1912fc4ca219a9cbb4ac5a485451c625a7ffcc1949fb8574a3f3d2
 DIST mira_3rdparty_09-09-2011.tar.bz2 31285 SHA256 0e00cd0efff5601d559ee8d40d29b8d3b87db3f4cd5b7bfa5970501ea43f840b SHA512 de000592c0ffcf834dc31d33603107bac4ab8ed29cdb4db8e6e8e73d024214a641718c2a917bd7c73b50c4047201d629fc1f82c1618487e62589d0b276f7462f WHIRLPOOL 94c2723218dd6378352b365d36cd488269abeadf09dd544f1fc40c3af31de5b6149a32f97c7365f1df8b947e7a6738fef0448f39a5d74b398e98c1a14f3ef4f3
diff --git a/sci-biology/mira/mira-3.4.0.1.ebuild b/sci-biology/mira/mira-3.4.0.1.ebuild
index 45d9911fb..88d150ac0 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 000000000..813eee057
--- /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"
+}