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-rw-r--r--sci-biology/biopython/ChangeLog346
-rw-r--r--sci-biology/biopython/Manifest1
-rw-r--r--sci-biology/biopython/biopython-1.62-r1.ebuild51
-rw-r--r--sci-biology/biopython/files/biopython-1.62-SffIO.patch36
-rw-r--r--sci-biology/biopython/metadata.xml5
-rw-r--r--sci-biology/mira/ChangeLog4
-rw-r--r--sci-biology/mira/Manifest1
-rw-r--r--sci-biology/mira/metadata.xml10
-rw-r--r--sci-biology/mira/mira-4.0_rc2.ebuild78
9 files changed, 527 insertions, 5 deletions
diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/ChangeLog
new file mode 100644
index 000000000..baf3b3a19
--- /dev/null
+++ b/sci-biology/biopython/ChangeLog
@@ -0,0 +1,346 @@
+# ChangeLog for sci-biology/biopython
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/ChangeLog,v 1.72 2013/09/17 16:07:56 jlec Exp $
+
+*biopython-1.62-r1 (25 Sep 2013)
+
+ 25 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +biopython-1.62-r1.ebuild, +files/biopython-1.51-flex.patch,
+ +files/biopython-1.62-SffIO.patch, +files/SeqRecord.py.patch,
+ +files/adjust-trimpoints.patch, +metadata.xml:
+ Upstream accidentally dropped some of my patch chunks while preparing 1.62
+ release. Bringing them back myself at least through sci overlay.
+
+*biopython-1.62 (17 Sep 2013)
+
+ 17 Sep 2013; Justin Lecher <jlec@gentoo.org> +biopython-1.62.ebuild:
+ Version Bump
+
+ 02 Jul 2013; Justin Lecher <jlec@gentoo.org> biopython-1.61.ebuild:
+ Fix deps for python
+
+ 06 Jun 2013; Justin Lecher <jlec@gentoo.org> biopython-1.61.ebuild:
+ Keyword ~-linux
+
+*biopython-1.61 (26 Apr 2013)
+
+ 26 Apr 2013; Justin Lecher <jlec@gentoo.org> +biopython-1.61.ebuild,
+ metadata.xml:
+ Version Bump
+
+ 14 Dec 2012; Ulrich Müller <ulm@gentoo.org> biopython-1.57.ebuild,
+ biopython-1.58.ebuild, biopython-1.59.ebuild:
+ Update LICENSE, HPND according to LICENSE file.
+
+*biopython-1.59 (27 Feb 2012)
+
+ 27 Feb 2012; Andrey Kislyuk <weaver@gentoo.org> +biopython-1.59.ebuild:
+ Version bump
+
+ 26 Dec 2011; Andrey Kislyuk <weaver@gentoo.org> +biopython-1.58.ebuild:
+ Version bump
+
+*biopython-1.58 (26 Dec 2011)
+
+ 26 Dec 2011; Andrey Kislyuk <weaver@gentoo.org> +biopython-1.58.ebuild:
+ Version bump
+
+ 23 Jun 2011; Markos Chandras <hwoarang@gentoo.org> -biopython-1.56.ebuild:
+ Remove old ebuilds. Requested by Arfrever
+
+ 28 May 2011; Brent Baude <ranger@gentoo.org> biopython-1.57.ebuild:
+ Marking biopython-1.57 ppc for bug 365877
+
+ 24 May 2011; Markus Meier <maekke@gentoo.org> biopython-1.57.ebuild:
+ x86 stable, bug #365877
+
+ 06 May 2011; Justin Lecher <jlec@gentoo.org> biopython-1.56.ebuild,
+ biopython-1.57.ebuild:
+ Cleaned DESCRIPTION
+
+ 05 May 2011; Markos Chandras <hwoarang@gentoo.org> biopython-1.57.ebuild:
+ Stable on amd64 wrt bug #365877
+
+*biopython-1.57 (03 Apr 2011)
+
+ 03 Apr 2011; Arfrever Frehtes Taifersar Arahesis <arfrever@gentoo.org>
+ +biopython-1.57.ebuild:
+ Version bump.
+
+ 30 Jan 2011; Arfrever Frehtes Taifersar Arahesis <arfrever@gentoo.org>
+ -biopython-1.55.ebuild:
+ Delete.
+
+ 30 Jan 2011; Raúl Porcel <armin76@gentoo.org> biopython-1.55.ebuild,
+ biopython-1.56.ebuild:
+ Drop alpha/sparc keywords
+
+ 15 Jan 2011; Pawel Hajdan jr <phajdan.jr@gentoo.org>
+ biopython-1.56.ebuild:
+ x86 stable wrt bug #351498
+
+ 14 Jan 2011; Brent Baude <ranger@gentoo.org> biopython-1.56.ebuild:
+ stable ppc, bug 351498
+
+ 13 Jan 2011; Markos Chandras <hwoarang@gentoo.org> biopython-1.56.ebuild:
+ Stable on amd64 wrt bug #351498
+
+ 06 Jan 2011; Brent Baude <ranger@gentoo.org> biopython-1.55.ebuild:
+ Marking biopython-1.55 ppc for bug 341519
+
+*biopython-1.56 (13 Dec 2010)
+
+ 13 Dec 2010; Arfrever Frehtes Taifersar Arahesis <arfrever@gentoo.org>
+ -biopython-1.53.ebuild, -biopython-1.54.ebuild, +biopython-1.56.ebuild:
+ Version bump.
+
+ 31 Oct 2010; Raúl Porcel <armin76@gentoo.org> biopython-1.55.ebuild:
+ alpha/sparc stable wrt #341519
+
+ 21 Oct 2010; Thomas Kahle <tomka@gentoo.org> biopython-1.55.ebuild:
+ x86 stable per bug 341519
+
+ 19 Oct 2010; Markos Chandras <hwoarang@gentoo.org> biopython-1.55.ebuild:
+ Stable on amd64 wrt bug #341519
+
+ 15 Oct 2010; Brent Baude <ranger@gentoo.org> biopython-1.54.ebuild:
+ stable ppc, bug 327151
+
+ 10 Oct 2010; Raúl Porcel <armin76@gentoo.org> biopython-1.54.ebuild:
+ sparc stable wrt #327151
+
+*biopython-1.55 (17 Sep 2010)
+
+ 17 Sep 2010; Arfrever Frehtes Taifersar Arahesis <arfrever@gentoo.org>
+ +biopython-1.55.ebuild:
+ Version bump.
+
+ 12 Sep 2010; Tobias Klausmann <klausman@gentoo.org> biopython-1.54.ebuild:
+ Stable on alpha, bug #327151
+
+ 12 Jul 2010; Christian Faulhammer <fauli@gentoo.org>
+ biopython-1.54.ebuild:
+ stable x86, bug 327151
+
+ 06 Jul 2010; Markos Chandras <hwoarang@gentoo.org> biopython-1.54.ebuild:
+ Stable on amd64 wrt bug #327151
+
+*biopython-1.54 (05 Jun 2010)
+
+ 05 Jun 2010; Arfrever Frehtes Taifersar Arahesis <arfrever@gentoo.org>
+ -biopython-1.49.ebuild, -files/biopython-1.49-flex.patch,
+ -biopython-1.51.ebuild, -biopython-1.52.ebuild, +biopython-1.54.ebuild:
+ Version bump.
+
+ 13 Feb 2010; Raúl Porcel <armin76@gentoo.org> biopython-1.53.ebuild:
+ alpha/sparc stable wrt #301964
+
+ 07 Feb 2010; Markus Meier <maekke@gentoo.org> biopython-1.53.ebuild:
+ amd64/x86 stable, bug #301964
+
+ 24 Jan 2010; Brent Baude <ranger@gentoo.org> biopython-1.53.ebuild:
+ stable ppc, bug 301964
+
+*biopython-1.53 (21 Dec 2009)
+
+ 21 Dec 2009; Arfrever Frehtes Taifersar Arahesis <arfrever@gentoo.org>
+ +biopython-1.53.ebuild:
+ Version bump. Set SUPPORT_PYTHON_ABIS.
+
+ 31 Oct 2009; Markus Meier <maekke@gentoo.org> biopython-1.52.ebuild:
+ amd64/x86 stable, bug #290931
+
+*biopython-1.52 (23 Sep 2009)
+
+ 23 Sep 2009; Andrey Kislyuk <weaver@gentoo.org> +biopython-1.52.ebuild:
+ Version bump
+
+*biopython-1.51 (09 Sep 2009)
+
+ 09 Sep 2009; Andrey Kislyuk <weaver@gentoo.org>
+ +files/biopython-1.51-flex.patch, +biopython-1.51.ebuild:
+ Version bump
+
+ 26 Aug 2009; Christian Faulhammer <fauli@gentoo.org> metadata.xml:
+ remove now unused flag description
+
+ 26 Aug 2009; Christian Faulhammer <fauli@gentoo.org>
+ -biopython-1.42.ebuild, -files/biopython-1.43-buildkdtree.patch,
+ -biopython-1.44.ebuild, -files/biopython-1.44-sequtils-complement.patch,
+ -biopython-1.47.ebuild, -files/biopython-1.47-kdtree.patch:
+ clean up
+
+ 26 Aug 2009; Tobias Klausmann <klausman@gentoo.org> biopython-1.49.ebuild:
+ Stable on alpha, bug #277822
+
+ 02 Aug 2009; nixnut <nixnut@gentoo.org> biopython-1.49.ebuild:
+ ppc stable #277822
+
+ 20 Jul 2009; Jeremy Olexa <darkside@gentoo.org> biopython-1.49.ebuild:
+ amd64 stable, bug 277822
+
+ 17 Jul 2009; Ferris McCormick <fmccor@gentoo.org> biopython-1.49.ebuild:
+ Sparc stable --- bug #277822 --- ran tests successfully.
+
+ 14 Jul 2009; Christian Faulhammer <fauli@gentoo.org>
+ biopython-1.49.ebuild:
+ stable x86, bug 277822
+
+ 24 Mar 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml:
+ Giving up maintainership of this package.
+
+*biopython-1.49 (16 Jan 2009)
+
+ 16 Jan 2009; Olivier Fisette <ribosome@gentoo.org>
+ +files/biopython-1.49-flex.patch, +biopython-1.49.ebuild:
+ Version bump. Thanks to Juan Aguado <juantxorena@gmail.com> for his work.
+ Fixes bug #248799.
+
+ 06 Aug 2008; Ulrich Mueller <ulm@gentoo.org> metadata.xml:
+ Add USE flag description to metadata wrt GLEP 56.
+
+ 14 Jul 2008; nixnut <nixnut@gentoo.org> biopython-1.44.ebuild:
+ Stable on ppc wrt bug 221159
+
+ 07 Jul 2008; Raúl Porcel <armin76@gentoo.org> biopython-1.44.ebuild:
+ alpha/sparc/x86 stable wrt #221159
+
+*biopython-1.47 (06 Jul 2008)
+
+ 06 Jul 2008; Olivier Fisette <ribosome@gentoo.org>
+ +files/biopython-1.47-kdtree.patch, +biopython-1.47.ebuild:
+ New version. Better documentation installation. Added scripts and test
+ suite. KDTree now enabled by default (requires switching to EAPI 1).
+
+ 06 Jul 2008; Olivier Fisette <ribosome@gentoo.org> biopython-1.44.ebuild:
+ Stable on amd64.
+
+ 30 Jan 2008; Olivier Fisette <ribosome@gentoo.org> biopython-1.42.ebuild,
+ biopython-1.44.ebuild:
+ Q.A.: Quoted variables.
+
+ 30 Jan 2008; Olivier Fisette <ribosome@gentoo.org> -biopython-1.43.ebuild:
+ Removed buggy version (see bug #202602).
+
+*biopython-1.44 (30 Jan 2008)
+
+ 30 Jan 2008; Olivier Fisette <ribosome@gentoo.org>
+ +files/biopython-1.44-sequtils-complement.patch, +biopython-1.44.ebuild:
+ Fixed six_frame_translations function. Thanks to JTRiley
+ <justin.t.riley@gmail.com> for his patch. (Fixes bug #202606.)
+
+*biopython-1.43 (17 May 2007)
+
+ 17 May 2007; Olivier Fisette <ribosome@gentoo.org>
+ +files/biopython-1.43-buildkdtree.patch, -biopython-1.40b.ebuild,
+ +biopython-1.43.ebuild:
+ New upstream version. Ebuild clean-up. Pruned old version.
+
+ 16 May 2007; Raúl Porcel <armin76@gentoo.org> biopython-1.42.ebuild:
+ alpha stable wrt #153774
+
+ 05 Nov 2006; Christian Faulhammer <opfer@gentoo.org>
+ biopython-1.42.ebuild:
+ stabled x86, bug #153774
+
+ 03 Nov 2006; <blubb@gentoo.org> biopython-1.42.ebuild:
+ stable on amd64
+
+ 03 Nov 2006; Olivier Fisette <ribosome@gentoo.org> -biopython-1.41.ebuild:
+ Pruned old version.
+
+ 02 Nov 2006; nixnut <nixnut@gentoo.org> biopython-1.42.ebuild:
+ Stable on ppc wrt bug 153774
+
+ 02 Nov 2006; Jason Wever <weeve@gentoo.org> biopython-1.42.ebuild:
+ Stable on SPARC wrt bug #153774.
+
+ 14 Sep 2006; Olivier Fisette <ribosome@gentoo.org> metadata.xml:
+ Taking over maintainership.
+
+*biopython-1.42 (12 Sep 2006)
+
+ 12 Sep 2006; Olivier Fisette <ribosome@gentoo.org> +biopython-1.42.ebuild:
+ New upstream version.
+
+ 19 Jan 2006; George Shapovalov <george@gentoo.org> +biopython-1.41.ebuild:
+ new version, cleaned up install
+
+ 30 Aug 2005; Olivier Fisette <ribosome@gentoo.org> -biopython-1.24.ebuild,
+ -biopython-1.30.ebuild:
+ Removed obsolete versions.
+
+ 12 Jun 2005; Bryan Østergaard <kloeri@gentoo.org> biopython-1.40b.ebuild:
+ Stable on alpha.
+
+ 21 May 2005; Jason Wever <weeve@gentoo.org> biopython-1.40b.ebuild:
+ Stable on SPARC.
+
+ 13 May 2005; Olivier Fisette <ribosome@gentoo.org> -biopython-1.10.ebuild,
+ -biopython-1.21.ebuild, -biopython-1.23.ebuild, biopython-1.40b.ebuild:
+ Removed obsolete versions. Added 1.40b to x86.
+
+*biopython-1.40b (19 Feb 2005)
+
+ 19 Feb 2005; Olivier Fisette <ribosome@gentoo.org>
+ +biopython-1.40b.ebuild:
+ New version. Should fix bug #82498.
+
+ 29 Dec 2004; Ciaran McCreesh <ciaranm@gentoo.org> :
+ Change encoding to UTF-8 for GLEP 31 compliance
+
+*biopython-1.23 (23 Dec 2004)
+
+ 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
+ +biopython-1.10.ebuild, +biopython-1.21.ebuild, +biopython-1.23.ebuild,
+ +biopython-1.24.ebuild, +biopython-1.30.ebuild:
+ Moved from app-sci/biopython to sci-biology/biopython.
+
+ 13 Dec 2004; Jason Wever <weeve@gentoo.org> biopython-1.24.ebuild:
+ Stable on sparc.
+
+*biopython-1.30 (07 Oct 2004)
+
+ 07 Oct 2004; George Shapovalvo <george@gentoo.org> biopython-1.30.ebuild :
+ new version (#51833)
+ amd64 has problems with KDTree, will try to look into this more later
+
+ 05 May 2004; Bryan Østergaard <kloeri@gentoo.org> biopython-1.24.ebuild:
+ Stable on alpha.
+
+ 03 Apr 2004; Peter Bienstman <pbienst@gentoo.org> biopython-1.24.ebuild:
+ Marked stable on x86
+
+*biopython-1.24 (29 Feb 2004)
+
+ 29 Feb 2004; Peter Bienstman <pbienst@gentoo.org> biopython-1.24.ebuild :
+ version bump
+
+*biopython-1.23 (30 Dec 2003)
+
+ 29 Feb 2004; Peter Bienstman <pbienst@gentoo.org> biopython-1.23.ebuild :
+ marked stable on x86
+
+ 30 Dec 2003; George Shapovalvo <george@gentoo.org> biopython-1.23.ebuild :
+ new version, reworked to use distutils. Thanks to
+ Peter Bienstman <Peter.Bienstman@rug.ac.be> for an update (#35727)
+
+ 02 Sep 2003; Alastair Tse <liquidx@gentoo.org> biopython-1.10.ebuild,
+ biopython-1.21.ebuild:
+ moved dev-python/Numeric to dev-python/numeric
+
+*biopython-1.21 (08 Aug 2003)
+
+ 08 Aug 2003; George Shapovalov <george@gentoo.org> biopython-1.21.ebuild :
+ new version, added few docs (#25428)
+ thanks to Daniel Jaeggi <daniel@jaeggi.co.uk> for notification
+
+ 04 Jul 2003; Alastair Tse <liquidx@gentoo.org> biopython-1.10.ebuild:
+ renamed reportlab dep
+
+*biopython-1.10 (18 Feb 2003)
+
+ 18 Feb 2003; George Shapovalov <george@gentoo.org> ChangeLog, biopython-1.10.ebuild, files/digest-biopython-1.10 :
+ initial release (#11617)
+ Biopython - python module for Computational Moelcular Biology
+ ebuild submitted by Daniel Jaeggi <daniel@jaeggi.co.uk>
diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest
new file mode 100644
index 000000000..0ac23ecd9
--- /dev/null
+++ b/sci-biology/biopython/Manifest
@@ -0,0 +1 @@
+DIST biopython-1.62.tar.gz 11389349 SHA256 b056414028c8cc0eea3de20d740f7a12ad0813b705de7dd454deec8f9ede52c6 SHA512 0178fd2c2e7b5e9a6cf05e8b8567bb0c1a93e9b05d5faa9802e0e2b0d59fc5e2ce9786c38cbbd00be5b35e4e4a3b41869e774a50cbbcdf6b34788c873cf0f3f2 WHIRLPOOL 63f61243581afee07cd9295989cb90b2221588e066eb1d5695da4b75fcd0abc95a9341ce07a8ffdfc3e85afdc6002582c589ac39e36e98ca4c8a257e63826351
diff --git a/sci-biology/biopython/biopython-1.62-r1.ebuild b/sci-biology/biopython/biopython-1.62-r1.ebuild
new file mode 100644
index 000000000..d3e61a264
--- /dev/null
+++ b/sci-biology/biopython/biopython-1.62-r1.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/biopython-1.62.ebuild,v 1.1 2013/09/17 16:07:56 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit distutils-r1 eutils
+
+DESCRIPTION="Python modules for computational molecular biology"
+HOMEPAGE="http://www.biopython.org/ http://pypi.python.org/pypi/biopython/"
+SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz"
+
+LICENSE="HPND"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE="mysql postgres"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="${PYTHON_DEPS}
+ dev-python/matplotlib[${PYTHON_USEDEP}]
+ dev-python/networkx[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/pygraphviz[${PYTHON_USEDEP}]
+ dev-python/reportlab[${PYTHON_USEDEP}]
+ media-gfx/pydot[${PYTHON_USEDEP}]
+ mysql? ( dev-python/mysql-python[${PYTHON_USEDEP}] )
+ postgres? ( dev-python/psycopg[${PYTHON_USEDEP}] )"
+DEPEND="${RDEPEND}
+ sys-devel/flex"
+
+DOCS=( CONTRIB DEPRECATED NEWS README Doc/. )
+
+src_prepare() {
+ distutils-r1_src_prepare
+ epatch "${FILESDIR}/${PN}-1.62-SffIO.patch"
+}
+
+python_test() {
+ cd Tests || die
+ ${PYTHON} run_tests.py || die
+}
+
+python_install_all() {
+ distutils-r1_python_install_all
+
+ dodir /usr/share/${PN}
+ cp -r --preserve=mode Scripts Tests "${ED}"/usr/share/${PN} || die
+}
diff --git a/sci-biology/biopython/files/biopython-1.62-SffIO.patch b/sci-biology/biopython/files/biopython-1.62-SffIO.patch
new file mode 100644
index 000000000..7f2208ef6
--- /dev/null
+++ b/sci-biology/biopython/files/biopython-1.62-SffIO.patch
@@ -0,0 +1,36 @@
+--- Bio/SeqIO/SffIO.py.ori 2013-09-25 13:28:51.000000000 +0200
++++ Bio/SeqIO/SffIO.py 2013-09-25 13:37:44.000000000 +0200
+@@ -383,7 +383,14 @@
+ if padding:
+ padding = 8 - padding
+ if handle.read(padding).count(_null) != padding:
+- raise ValueError("Post quality %i byte padding region contained data"
++ import warnings
++ from Bio import BiopythonParserWarning
++ warnings.warn("Your SFF file is valid but post quality %i byte "
++ "padding region contains UNUSED data. Was the "
++ "SFF file created by SRA sff-dump >2.1.7 and <2.1.10? "
++ "It did not clear some internal buffer while writing "
++ "out new data so that previous values remained in the"
++ "output unless overwritten by new real values."
+ % padding)
+ #print read, name, record_offset
+ yield name, record_offset
+--- Bio/SeqIO/SffIO.py.ori 2013-09-25 14:07:14.000000000 +0200
++++ Bio/SeqIO/SffIO.py 2013-09-25 14:08:59.000000000 +0200
+@@ -596,7 +596,14 @@
+ if padding:
+ padding = 8 - padding
+ if handle.read(padding).count(_null) != padding:
+- raise ValueError("Post quality %i byte padding region contained data"
++ import warnings
++ from Bio import BiopythonParserWarning
++ warnings.warn("Your SFF file is valid but post quality %i byte "
++ "padding region contains UNUSED data. Was the "
++ "SFF file created by SRA sff-dump >2.1.7 and <2.1.10? "
++ "It did not clear some internal buffer while writing "
++ "out new data so that previous values remained in the"
++ "output unless overwritten by new real values."
+ % padding)
+ #Follow Roche and apply most aggressive of qual and adapter clipping.
+ #Note Roche seems to ignore adapter clip fields when writing SFF,
diff --git a/sci-biology/biopython/metadata.xml b/sci-biology/biopython/metadata.xml
new file mode 100644
index 000000000..f17a827e3
--- /dev/null
+++ b/sci-biology/biopython/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog
index afda6bd66..bd7298590 100644
--- a/sci-biology/mira/ChangeLog
+++ b/sci-biology/mira/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 25 Sep 2013; Justin Lecher <jlec@gentoo.org> mira-4.0_rc2.ebuild,
+ metadata.xml:
+ Fix m4 macrodir location
+
*mira-3.9.15 (30 Apr 2013)
30 Apr 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/mira/Manifest b/sci-biology/mira/Manifest
index d25adbba0..4d5034710 100644
--- a/sci-biology/mira/Manifest
+++ b/sci-biology/mira/Manifest
@@ -2,5 +2,6 @@ DIST mira-3.4.0.1.tar.bz2 10262667 SHA256 cafe45601b3c143ac142c022e1fc0a21544e88
DIST mira-3.4.1.1.tar.gz 11665587 SHA256 d523a75ea499886564c2f698397c21d49e970e3d4f773b7fd13098f8f20ccce8 SHA512 f7ecf942b168f0a7b32505dfbc625c6fbded00084ae7511e59d0b236ca8b76deba712ea09239d12aeb3190daf6faecce714cd6bceb02edcbc5df44d021bf36f3 WHIRLPOOL 44bc92e5b02536cbdd09fb08566e7d885cab75a6841d8826450ef1a7e7dcf797a4c77e482c3fadedc8422e93292ea7781705a16a6bc3d848675b717ca60e722f
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_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/metadata.xml b/sci-biology/mira/metadata.xml
index 07b525505..2bc893037 100644
--- a/sci-biology/mira/metadata.xml
+++ b/sci-biology/mira/metadata.xml
@@ -1,9 +1,9 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <herd>sci-biology</herd>
- <maintainer>
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
</pkgmetadata>
diff --git a/sci-biology/mira/mira-4.0_rc2.ebuild b/sci-biology/mira/mira-4.0_rc2.ebuild
new file mode 100644
index 000000000..48a135a29
--- /dev/null
+++ b/sci-biology/mira/mira-4.0_rc2.ebuild
@@ -0,0 +1,78 @@
+# 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"
+
+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/mira-4.0rc2.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}/mira-4.0rc2"
+
+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
+
+ sed \
+ -e 's:m4:config/m4:g' \
+ -i Makefile.am 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"
+}