4 files changed, 27 insertions, 128 deletions
diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog
index 00fa076f6b44..aca95afca34a 100644
--- a/sci-biology/mira/ChangeLog
+++ b/sci-biology/mira/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/mira
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/ChangeLog,v 1.22 2013/07/07 19:41:05 jlec Exp $
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/ChangeLog,v 1.23 2014/01/06 08:58:27 jlec Exp $
+
+  06 Jan 2014; Justin Lecher <jlec@gentoo.org> -mira-3.2.1-r1.ebuild,
+  -mira-3.4.0.2.ebuild:
+  Drop old
 
 *mira-3.9.18 (07 Jul 2013)
 
diff --git a/sci-biology/mira/Manifest b/sci-biology/mira/Manifest
index 7a684b7bd711..87576565f763 100644
--- a/sci-biology/mira/Manifest
+++ b/sci-biology/mira/Manifest
@@ -1,14 +1,31 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA512
+
 AUX mira-3.0.0-asneeded.patch 1468 SHA256 17dec784921baccf2c515f7c269209b5cdeb23143b3412e8ad967e74682ee71f SHA512 23f151eb138a216f329b9fefc8b014391915dd5d578b36ac87b4b7f52277313ae8081011b6839882dcb991524ad674ff22bfd7d6d2a91d28f9e5ff19d41e2f3d WHIRLPOOL b3d37aa5b5963cd75a9c9d4d513351c408aa315f40a07acfb8b8c1998f032ad3df50819786e8f31c7c411cd07b08f1609b4e9f78e4305a97eaf23255a3893ec5
 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-3.2.1.tar.bz2 9626154 SHA256 86a2c00d182573008ef41f7725aec72ea69756ea9f3dc7e798a7d253a47f8bd7 SHA512 56b2bac26d86f1c6a1aef829e168e53d931e6211078966e4ce5464ef26fbce4395c448521bf7d35f74080c00b4efbf6597b2713b276f04683433c32fdcb1199d WHIRLPOOL 85531afa6f7593de938c922e88871104bdd837271448615a23fcd2042b71e1ef9b7900f1906bb64349cad17f4f66f3d958e6aa2148239738e4c45d320a01185f
-DIST mira-3.4.0.2.tar.bz2 10225270 SHA256 5cf24fc6760723b7b8d4d239ee25eb5471e50080aa9bca2c1b01a30be6ae808c SHA512 3d74af98fa1a72892a04579110a74d986170572aca42983e5526ff58a76f2defdacee8d9a5e61cfc685639d41197308493e733aa8b527eba74d21942ca4dc7db WHIRLPOOL 2935ddfe542960d586cfa010cd4e6849d2e9765c4bca384adde38fae4ac95ee654f552958148b3f0d6d27a81246d7443ee6979b5723a959284c5ee39061c78cf
 DIST mira-3.9.18.tar.bz2 10378027 SHA256 ca8236b570cf8d3eabfc394edea33a3406e9e8b9e0b8aca9a418d20679710747 SHA512 99bfc0200f8220bdd4ddffb608d2e4e2bf9554cda0f7934c5252e22b01fa93b12105e3e55d59c994ef004d71c0396170ff170bd7494250c961e150123349b914 WHIRLPOOL 90e6016e62b28d5ac681a7da4ae81363da74137002dc6c19e23c8b53a777cd020d727ac2dfd67f126728317ece7b51ea4dab153a720e37b6ac31aa07d5b633b9
 DIST mira_3rdparty_06-07-2012.tar.bz2 31656 SHA256 53cbbb9d57e2fa51706b3f1d055621c0863091542b8851f3ce8a45850951d7d2 SHA512 4d4dbdf7ab5126f9d47160bee8bc127b6a225de8087f6b9914c754324a74d966333207c86a3f38cf0ea9f91408707e2a24086dbe1318fdfa2870b0c39bc5033b WHIRLPOOL c9946ddc032d6864a33e7a60a4d1a515262ca2204535c7d81dcc73144b4f471f766007082d1912fc4ca219a9cbb4ac5a485451c625a7ffcc1949fb8574a3f3d2
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-EBUILD mira-3.2.1-r1.ebuild 1713 SHA256 9ca51eaec1d05fbb7b90c65f872b9d1be7fd679d5dbcb0195232889a8188ef9e SHA512 e229acd584521c4731d9481fd0c9936a0a2f55067d3b8624eb02ee2b95122927c6a0d22efb4d9bf113020f29cf52f950d3de8ce0f9a78ef2d6d192b62ba7a6d8 WHIRLPOOL 5d6fa960e8df74021b601223c3fb3bd2fd0e1709dae1d4bcbabd49e889252733ca710ff89940e3facc4c031531f284ebb9c75c071b440623be89bf096ae5fc4c
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-EBUILD mira-3.4.0.2.ebuild 1689 SHA256 3d3a8c5882e7e2d012cc1d1af521c4ad63cfc11b57da84b29bb3fe8aeb06e63a SHA512 2ef505866e0d1d81f981c307082987e4a0d496cec8976f1cd51905d22e818d459e5b5d4cf97d015b2040f46e2f149107a0ca05031fea1c4bee2cf42d0c848779 WHIRLPOOL ef9712b1086cb5280e45396c0a99053227f021d5f8ef19b4bde4ba034a0f2a35b6b065b9eb187a48b3d7330b546929516d65adec4263157fad5341c76fdffea6
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diff --git a/sci-biology/mira/mira-3.2.1-r1.ebuild b/sci-biology/mira/mira-3.2.1-r1.ebuild
deleted file mode 100644
index b4d434df4a9b..000000000000
--- a/sci-biology/mira/mira-3.2.1-r1.ebuild
+++ /dev/null
@@ -1,61 +0,0 @@
-# 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 1.2 2012/11/07 22:29:55 jlec Exp $
-
-EAPI=4
-
-MIRA_3RDPARTY_PV="17-04-2010"
-
-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="${CDEPEND}
-	dev-libs/expat"
-RDEPEND="${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}-3.0.0-asneeded.patch \
-		"${FILESDIR}"/${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"
-}
diff --git a/sci-biology/mira/mira-3.4.0.2.ebuild b/sci-biology/mira/mira-3.4.0.2.ebuild
deleted file mode 100644
index e3582fddd25c..000000000000
--- a/sci-biology/mira/mira-3.4.0.2.ebuild
+++ /dev/null
@@ -1,61 +0,0 @@
-# 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"
-}