sci-biology/mira: Version BUmp, thanks Martin Mokrejš for the work

Package-Manager: portage-2.2.15/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

3 files changed, 99 insertions, 16 deletions

diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog
index 59b0cb700be8..30fd80586652 100644
--- a/sci-biology/mira/ChangeLog
+++ b/sci-biology/mira/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/mira
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/ChangeLog,v 1.28 2015/01/23 11:25:31 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/ChangeLog,v 1.29 2015/01/23 11:48:13 jlec Exp $
+
+*mira-4.0.2 (23 Jan 2015)
+
+  23 Jan 2015; Justin Lecher <jlec@gentoo.org> +mira-4.0.2.ebuild:
+  Version BUmp, thanks Martin Mokrejš for the work
 
   23 Jan 2015; Justin Lecher <jlec@gentoo.org> mira-3.9.18.ebuild:
   Add workaroung for m4 dir location, #536172
diff --git a/sci-biology/mira/Manifest b/sci-biology/mira/Manifest
index 9d7c3d3ee0af..35cbc958917f 100644
--- a/sci-biology/mira/Manifest
+++ b/sci-biology/mira/Manifest
@@ -5,26 +5,28 @@ AUX mira-3.0.0-asneeded.patch 1468 SHA256 17dec784921baccf2c515f7c269209b5cdeb23
 AUX mira-3.2.1-boost-1.50.patch 3672 SHA256 35bebb987d6192889a1cce84fae822e61d607e80cbaadb0ff1703935f8707ead SHA512 5b0cee936ca68ac57c6c8da4b8ab60e582f6ea1b89f5e02eae5562cd299b5f7bffe12454b55088da46d0e04212499aea72f3702619c9854d99792eb27f7b8995 WHIRLPOOL 08636d66e3d1443c392f798d61f7041ffdb727cb96d1a980e6091217577f75c1703cb172f8dc5d511ef2854e531e0af77bc2a8b58126f991010b7fc7e2877718
 AUX mira-3.4.0.2-boost-1.50.patch 1577 SHA256 66edfe52daf8e84844f20d7425b476a8fae95704226493bced687fd1026ec8e6 SHA512 60e8da6d56385114056f16292fb8e6de63498dbd587b12c26724d9007e8f7eea7550f1dac387035768d7fa76fdffcc7c5baac9b0f92b58bec8c269cf3f397cdf WHIRLPOOL 2fe35917e9b7a8f66ef30b19afc495ffba391aef0e64c695d2733959b12119b2b45d6e79390721e794fcb6bc029af71e3c84bf657bf5e485a1ca8295208623ea
 DIST mira-3.9.18.tar.bz2 10378027 SHA256 ca8236b570cf8d3eabfc394edea33a3406e9e8b9e0b8aca9a418d20679710747 SHA512 99bfc0200f8220bdd4ddffb608d2e4e2bf9554cda0f7934c5252e22b01fa93b12105e3e55d59c994ef004d71c0396170ff170bd7494250c961e150123349b914 WHIRLPOOL 90e6016e62b28d5ac681a7da4ae81363da74137002dc6c19e23c8b53a777cd020d727ac2dfd67f126728317ece7b51ea4dab153a720e37b6ac31aa07d5b633b9
+DIST mira-4.0.2.tar.bz2 10368046 SHA256 a32cb2b21e0968a5536446287c895fe9e03d11d78957554e355c1080b7b92a80 SHA512 a7f9845de207cefb87ffa652f4f6b9b85735ef22eeb29b456e4d946ba1675e7dd2c78abb2da56f11fddcb699f5c0700a08ce298196ce1a8e586a758a8d3bdc7e WHIRLPOOL d038472f9b129e97883f59c471df51f07315ee38eda5a9e804cdd2d33988306162b1bb1dde2cb7fd510c82be5734240dfd69364d39865a47af439762c7154747
 DIST mira_3rdparty_06-07-2012.tar.bz2 31656 SHA256 53cbbb9d57e2fa51706b3f1d055621c0863091542b8851f3ce8a45850951d7d2 SHA512 4d4dbdf7ab5126f9d47160bee8bc127b6a225de8087f6b9914c754324a74d966333207c86a3f38cf0ea9f91408707e2a24086dbe1318fdfa2870b0c39bc5033b WHIRLPOOL c9946ddc032d6864a33e7a60a4d1a515262ca2204535c7d81dcc73144b4f471f766007082d1912fc4ca219a9cbb4ac5a485451c625a7ffcc1949fb8574a3f3d2
 EBUILD mira-3.9.18.ebuild 1979 SHA256 14a5fa4f5d6659fbad572a10de8d4f11340ac111a8e0b681818acceab94792ea SHA512 f63805561a477dd9878a3c397aeefb4bb0f393be5f14006c938e63d97b5f1093c62797838d2f15cccd7af91060fa56ed8fbdf307d358f5d12c141de6041ddc0b WHIRLPOOL 5fa51e5e01c71130269581faed7cd5e457e7431340fd7aef5ef60541c8d5f27144922adb2ebdf345e95fe7c3a6dceea0f429b22ba5d73b39783e7d530706bf3c
-MISC ChangeLog 3878 SHA256 08a9ac5a00ef032bbc5a9654508565014dd084ac6978eaa2527c5c75ae523bcf SHA512 a7726f860d882099ec4c80f36c83757ca20efab5c50609552be72d20b7be6dd8081fbca98f4ecb802b93f6e89e5674c8df12223ad37df2782ef889514ef29465 WHIRLPOOL c04a44ab7d30a5b507f87a9a5de5abcb447183fdfce4171b6c18917a347110c32c3cebad01b57937a968226d158dbdcec4a66908a14f9b39156a7599f3bbb5fa
+EBUILD mira-4.0.2.ebuild 2253 SHA256 e4d710f2f7348c930eccb293b6fd4aa866369af83f5a48a1e90d2de2b4abf32d SHA512 864cb73be0e9af2a6036008b9e69b95be9d459da9ab901b8ad1ba95fd97886ec5f138e8071a04f40a9e77af73096f8dbda4c0081af51dd6caf9a4dfe2c39003e WHIRLPOOL a5a858b4251413b85971352fe2b0ee5dbf33c0749a59bfe8ff5e2fa4b6d21b3a974bec61f5c88bda0f32e055d2301ebfcd4f59f5fcc45d8139b04931cf9659fd
+MISC ChangeLog 4025 SHA256 2178f6f60fec6be0d23742c560b111c6374c0b2dce21e4a50206ad545eed5bee SHA512 9035947627dba09389a5ee01606e90720cd45b9a6ee568734c9ca7dc7f664cdfa03df5394f4e1f5355fa48d2d00fd7198092339fd3ad1ceff54fae2d4d24b423 WHIRLPOOL b321a150fb4396b235c06978f6b775906b3970991e32a13bdd3714bd4278d86c73eb31621b36464739a7b53bafb6ad47a0777c48f9d1146fa9689a5bd34f0539
 MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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diff --git a/sci-biology/mira/mira-4.0.2.ebuild b/sci-biology/mira/mira-4.0.2.ebuild
new file mode 100644
index 000000000000..8ae345aeeef5
--- /dev/null
+++ b/sci-biology/mira/mira-4.0.2.ebuild
@@ -0,0 +1,76 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-4.0.2.ebuild,v 1.1 2015/01/23 11:48:13 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"
+}