14 files changed, 368 insertions, 0 deletions
diff --git a/sci-biology/cd-hit-auxtools/ChangeLog b/sci-biology/cd-hit-auxtools/ChangeLog
new file mode 100644
index 000000000..330e8541f
--- /dev/null
+++ b/sci-biology/cd-hit-auxtools/ChangeLog
@@ -0,0 +1,14 @@
+# ChangeLog for sci-biology/cd-hit-auxtools
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  01 Jun 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  cd-hit-auxtools-0.5.ebuild:
+  sci-biology/cd-hit-auxtools: added HTML manual page
+
+*cd-hit-auxtools-0.5 (01 Jun 2014)
+
+  01 Jun 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +cd-hit-auxtools-0.5.ebuild, +files/0.5-gentoo.patch, +metadata.xml:
+  sci-biology/cd-hit-auxtools: new package, needs gcc<=4.6.4 or some CXXFLAG to
+  loosen g++ strictness
diff --git a/sci-biology/cd-hit-auxtools/Manifest b/sci-biology/cd-hit-auxtools/Manifest
new file mode 100644
index 000000000..628b4cbe9
--- /dev/null
+++ b/sci-biology/cd-hit-auxtools/Manifest
@@ -0,0 +1,2 @@
+DIST cd-hit-auxtools-manual.html 27123 SHA256 a17d1ff54f061ced8b3f797238ee5596330cb2fdb237d8fbfdff7e2c47c06d14 SHA512 8b7b646ac63cb4cc888a2b3db0ef2e1feb215189b9a52ed5a760ad5dd1af4f0a0f7722b3fa7b634f8a84e3154622c4336401dfefc45fe614770917ef1d59429a WHIRLPOOL 1b8149b66353ce58f074f412a33726b583497da2b204377e9b639eb2082e78c442e68af3b9d6bcba324373755b75a4b3aa51516f5f771e7d65d14675e76916f6
+DIST cd-hit-auxtools-v0.5-2012-03-07.tgz 97230 SHA256 acacb96344eeab2a7cb20613961f0355eba1f5c1f5793f100a252c8c45e4a6ad SHA512 5b00ff4951c9f2b85b23bad7eae484c060f05df8a20c35bf1cff0bae770a6552b7ed19c90bbc36204ea3ba1722490c8ba654c7ec1b1d55f743afbc82be53ef5b WHIRLPOOL d5ff22b2c1fa77089e4543c905e3dacd37769d5e07b2a1ac85651ea8b057d39bf44997590afb12e4757a3482bebc0a63233272c2ae0e95eb88c584dcc0c49084
diff --git a/sci-biology/cd-hit-auxtools/cd-hit-auxtools-0.5.ebuild b/sci-biology/cd-hit-auxtools/cd-hit-auxtools-0.5.ebuild
new file mode 100644
index 000000000..e220e16a8
--- /dev/null
+++ b/sci-biology/cd-hit-auxtools/cd-hit-auxtools-0.5.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/cd-hit/cd-hit-4.6.ebuild,v 1.1 2012/06/20 18:39:24 jlec Exp $
+
+EAPI=4
+
+inherit eutils flag-o-matic toolchain-funcs
+
+RELDATE="2012-03-07"
+RELEASE="${PN}-v${PV}-${RELDATE}"
+
+DESCRIPTION="Additional cd-hit itools: read-linker, cd-hit-lap and cd-hit-dup"
+HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/"
+SRC_URI="http://cdhit.googlecode.com/files/${RELEASE}.tgz
+	http://weizhong-lab.ucsd.edu/cd-hit/wiki/doku.php?id=cd-hit-auxtools-manual -> cd-hit-auxtools-manual.html"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+LICENSE="GPL-2"
+IUSE="doc openmp"
+
+S="${WORKDIR}"/${RELEASE}
+
+pkg_setup() {
+	 use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler"
+}
+
+src_prepare() {
+	tc-export CXX
+	use openmp || append-flags -DNO_OPENMP
+	epatch "${FILESDIR}"/${PV}-gentoo.patch
+}
+
+src_compile() {
+	local myconf=
+	use openmp && myconf="openmp=yes"
+	make ${myconf} || die "If compilation failed try gcc-4.6.4 or older, newer versions are too picky about quality of the source code"
+}
+
+src_install() {
+	dodir /usr/bin
+	dobin read-linker cd-hit-lap cd-hit-dup
+	use doc && dodoc "${DISTDIR}"/cd-hit-auxtools-manual.html
+}
diff --git a/sci-biology/cd-hit-auxtools/files/0.5-gentoo.patch b/sci-biology/cd-hit-auxtools/files/0.5-gentoo.patch
new file mode 100644
index 000000000..3977cbee3
--- /dev/null
+++ b/sci-biology/cd-hit-auxtools/files/0.5-gentoo.patch
@@ -0,0 +1,47 @@
+--- Makefile.ori	2014-06-01 20:25:53.000000000 +0200
++++ Makefile	2014-06-01 20:27:15.000000000 +0200
+@@ -1,8 +1,8 @@
+ 
+-CC = g++
++CXX = g++
+ 
+-CFLAGS = -Wall -Wno-unused -I. -Imintlib
+-LFLAGS = -fPIC
++CXXFLAGS = -I. -Imintlib
++LDFLAGS = -fPIC
+ 
+ 
+ UNAME = $(shell uname)
+@@ -16,9 +16,9 @@
+ endif
+ 
+ ifeq ($(debug),yes)
+-CFLAGS += -ggdb
++CiXXFLAGS +=
+ else
+-CFLAGS += -O2
++CXXFLAGS +=
+ endif
+ 
+ 
+@@ -32,16 +32,16 @@
+ .SUFFIXES: .c .obj .cpp .cc .cxx .C
+ 
+ .cxx.o:
+-	$(CC) -c $(CFLAGS) -o $@ $<
++	$(CXX) -c $(CXXFLAGS) -o $@ $<
+ 
+ cd-hit-dup: $(OBJECTS) cdhit-dup.o
+-	$(CC) $(LFLAGS) $(OBJECTS) cdhit-dup.o -o cd-hit-dup
++	$(CXX) $(LDFLAGS) $(OBJECTS) cdhit-dup.o -o cd-hit-dup
+ 
+ cd-hit-lap: $(OBJECTS) cdhit-lap.o
+-	$(CC) $(LFLAGS) $(OBJECTS) cdhit-lap.o -o cd-hit-lap
++	$(CXX) $(LDFLAGS) $(OBJECTS) cdhit-lap.o -o cd-hit-lap
+ 
+ read-linker: $(OBJECTS) read-linker.o
+-	$(CC) $(LFLAGS) $(OBJECTS) read-linker.o -o read-linker
++	$(CXX) $(LDFLAGS) $(OBJECTS) read-linker.o -o read-linker
+ 
+ clean:
+ 	rm $(OBJECTS) cdhit-dup.o cdhit-lap.o read-linker.o
diff --git a/sci-biology/cd-hit-auxtools/metadata.xml b/sci-biology/cd-hit-auxtools/metadata.xml
new file mode 100644
index 000000000..2bc893037
--- /dev/null
+++ b/sci-biology/cd-hit-auxtools/metadata.xml
@@ -0,0 +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>
+</pkgmetadata>
diff --git a/sci-biology/cd-hit/ChangeLog b/sci-biology/cd-hit/ChangeLog
new file mode 100644
index 000000000..3c40aa1c8
--- /dev/null
+++ b/sci-biology/cd-hit/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for sci-biology/cd-hit
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  01 Jun 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> cd-hit-4.6.1.ebuild:
+  sci-biology/cd-hit-4.6.1: forgot to re-enable the reworked patch
+
+*cd-hit-4.6.1 (01 Jun 2014)
+
+  01 Jun 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +cd-hit-4.6.1.ebuild, +files/4.6.1-gentoo.patch, +metadata.xml:
+  sci-biology/cd-hit-4.6.1: version bump
diff --git a/sci-biology/cd-hit/Manifest b/sci-biology/cd-hit/Manifest
new file mode 100644
index 000000000..e3691a860
--- /dev/null
+++ b/sci-biology/cd-hit/Manifest
@@ -0,0 +1 @@
+DIST cd-hit-v4.6.1-2012-08-27.tgz 652425 SHA256 5e26431892609511992542c39705a1427e2fd6a526241977c527dfc74f795932 SHA512 5c353d151a7999d4ca6864fa9b987493315ed0dc10d64012ada219889f53f317098dbbf7cbff30653a40e4e2953b3b0addaba8fe08895c509e39efe9f8f23d90 WHIRLPOOL 3e5d4432f29da9cc0a300bf1d8d485e42a09bc426ccca7ac8ea0079759a23757171145c2977b07a5a83944c4f2c4e06acccddc1d80e82cd1383c31e1d43cb9bf
diff --git a/sci-biology/cd-hit/cd-hit-4.6.1.ebuild b/sci-biology/cd-hit/cd-hit-4.6.1.ebuild
new file mode 100644
index 000000000..d7c573fa0
--- /dev/null
+++ b/sci-biology/cd-hit/cd-hit-4.6.1.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/cd-hit/cd-hit-4.6.ebuild,v 1.1 2012/06/20 18:39:24 jlec Exp $
+
+EAPI=4
+
+inherit eutils flag-o-matic toolchain-funcs
+
+RELDATE="2012-08-27"
+RELEASE="${PN}-v${PV}-${RELDATE}"
+
+DESCRIPTION="Clustering Database at High Identity with Tolerance"
+HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/"
+SRC_URI="http://cdhit.googlecode.com/files/${RELEASE}.tgz"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+LICENSE="GPL-2"
+IUSE="doc openmp"
+
+S="${WORKDIR}"/${RELEASE}
+
+pkg_setup() {
+	 use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler"
+}
+
+src_prepare() {
+	tc-export CXX
+	use openmp || append-flags -DNO_OPENMP
+	epatch "${FILESDIR}"/${PV}-gentoo.patch
+}
+
+src_compile() {
+	local myconf=
+	use openmp && myconf="openmp=yes"
+	emake ${myconf}
+}
+
+src_install() {
+	dodir /usr/bin
+	emake PREFIX="${ED}/usr/bin" install
+	dodoc ChangeLog
+	use doc && dodoc doc/*
+}
diff --git a/sci-biology/cd-hit/files/4.6.1-gentoo.patch b/sci-biology/cd-hit/files/4.6.1-gentoo.patch
new file mode 100644
index 000000000..d9db28ca8
--- /dev/null
+++ b/sci-biology/cd-hit/files/4.6.1-gentoo.patch
@@ -0,0 +1,118 @@
+--- Makefile.ori	2014-06-01 20:12:44.000000000 +0200
++++ Makefile	2014-06-01 20:16:34.000000000 +0200
+@@ -1,16 +1,13 @@
+-
+-CC = g++ -Wall -ggdb
+-CC = g++ -pg
+-CC = g++
++CXX ?= g++
+ 
+ # without OpenMP
+-CCFLAGS = -DNO_OPENMP
++#CXXFLAGS = -DNO_OPENMP
+ 
+ # with OpenMP
+ # in command line: 
+ # make openmp=yes
+ ifeq ($(openmp),yes)
+-CCFLAGS = -fopenmp
++CXXFLAGS += -fopenmp
+ endif
+ 
+ # support debugging
+@@ -18,17 +15,17 @@
+ # make debug=yes
+ # make openmp=yes debug=yes
+ ifeq ($(debug),yes)
+-CCFLAGS += -ggdb
++CXXFLAGS +=
+ else
+-CCFLAGS += -O2
++CXXFLAGS +=
+ endif
+ 
+ ifdef MAX_SEQ
+-CCFLAGS += -DMAX_SEQ=$(MAX_SEQ)
++CXXFLAGS += -DMAX_SEQ=$(MAX_SEQ)
+ endif
+ 
+ #LDFLAGS = -static -o
+-LDFLAGS += -o
++#LDFLAGS += -o
+ 
+ PROGS = cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454
+ 
+@@ -36,7 +33,7 @@
+ CCFLAGS := $(CPPFLAGS) $(CCFLAGS) $(CXXFLAGS)
+ 
+ .c++.o:
+-	$(CC) $(CCFLAGS) -c $<
++	$(CXX) $(CXXFLAGS) -c $<
+ 
+ all: $(PROGS)
+ 
+@@ -46,49 +43,49 @@
+ # programs
+ 
+ cd-hit: cdhit-common.o cdhit-utility.o cdhit.o
+-	$(CC) $(CCFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit.o cdhit-common.o cdhit-utility.o -o cd-hit
+ 
+ cd-hit-2d: cdhit-common.o cdhit-utility.o cdhit-2d.o
+-	$(CC) $(CCFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-2d
+ 
+ cd-hit-est: cdhit-common.o cdhit-utility.o cdhit-est.o
+-	$(CC) $(CCFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o -o cd-hit-est
+ 
+ cd-hit-est-2d: cdhit-common.o cdhit-utility.o cdhit-est-2d.o
+-	$(CC) $(CCFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-est-2d
+ 
+ cd-hit-div: cdhit-common.o cdhit-utility.o cdhit-div.o
+-	$(CC) $(CCFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o -o cd-hit-div
+ 
+ cd-hit-454: cdhit-common.o cdhit-utility.o cdhit-454.o
+-	$(CC) $(CCFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-454
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o -o cd-hit-454
+ 
+ # objects
+ cdhit-common.o: cdhit-common.c++ cdhit-common.h
+-	$(CC) $(CCFLAGS) cdhit-common.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-common.c++ -c
+ 
+ cdhit-utility.o: cdhit-utility.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit-utility.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-utility.c++ -c
+ 
+ cdhit.o: cdhit.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit.c++ -c
+ 
+ cdhit-2d.o: cdhit-2d.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit-2d.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-2d.c++ -c
+ 
+ cdhit-est.o: cdhit-est.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit-est.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-est.c++ -c
+ 
+ cdhit-est-2d.o: cdhit-est-2d.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit-est-2d.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-est-2d.c++ -c
+ 
+ cdhit-div.o: cdhit-div.c++ cdhit-common.h
+-	$(CC) $(CCFLAGS) cdhit-div.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-div.c++ -c
+ 
+ cdhit-454.o: cdhit-454.c++ cdhit-common.h
+-	$(CC) $(CCFLAGS) cdhit-454.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-454.c++ -c
+ 
+-PREFIX ?= /usr/local/bin
++PREFIX ?= $(DESTDIR)/usr/bin
+ 
+ install:
+ 	for prog in $(PROGS); do \
diff --git a/sci-biology/cd-hit/metadata.xml b/sci-biology/cd-hit/metadata.xml
new file mode 100644
index 000000000..bd5607ab1
--- /dev/null
+++ b/sci-biology/cd-hit/metadata.xml
@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci-biology</herd>
+	<longdescription>
+CD-HIT is a very widely used program for clustering and comparing large sets 
+of protein or nucleotide sequences. CD-HIT is very fast and can handle 
+extremely large databases. CD-HIT helps to significantly reduce the 
+computational and manual efforts in many sequence analysis tasks and aids in 
+understanding the data structure and correct the bias within a dataset.
+The CD-HIT package has CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D, 
+CD-HIT-454, CD-HIT-PARA, PSI-CD-HIT and over a dozen scripts. CD-HIT 
+(CD-HIT-EST) clusters similar proteins (DNAs) into clusters that meet a 
+user-defined similarity threshold. CD-HIT-2D (CD-HIT-EST-2D) compares 2 
+datasets and identifies the sequences in db2 that are similar to db1 above 
+a threshold. CD-HIT-454 is a program to identify natural and artificial 
+duplicates from pyrosequencing reads. The usage of other programs and 
+scripts can be found in CD-HIT user's guide.
+</longdescription>
+	<upstream>
+		<remote-id type="google-code">cdhit</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-biology/ugene/ChangeLog b/sci-biology/ugene/ChangeLog
new file mode 100644
index 000000000..cff7871ab
--- /dev/null
+++ b/sci-biology/ugene/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/ugene
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*ugene-1.13.3 (01 Jun 2014)
+
+  01 Jun 2014; Alexey Shvetsov <alexxy@gentoo.org> +metadata.xml,
+  +ugene-1.13.3.ebuild:
+  Add new ebuild
diff --git a/sci-biology/ugene/Manifest b/sci-biology/ugene/Manifest
new file mode 100644
index 000000000..0ea7da6f4
--- /dev/null
+++ b/sci-biology/ugene/Manifest
@@ -0,0 +1 @@
+DIST ugene-1.13.3.tar.gz 19098687 SHA256 043a6b3c6dcb9cb872bf2cd335e40a479ae62d333099e6cbe7ddd3663abda611 SHA512 6ae3645d25e37ee40d0e383dca1c6e0c05f388d3486326be24f5ecea9d7c8a2e1f82c302c21567339e47cd4d0fe404bfe1ada00fb7c7d2e5fc8e790e2d7c582b WHIRLPOOL 1b774e6e1e7c17de6c766bd3d97a024abee65e0a6061530e9e466f3597500c7f027ec91582363409576bda89316cbe7b01c784588844d8735f65dd2d4181b435
diff --git a/sci-biology/ugene/metadata.xml b/sci-biology/ugene/metadata.xml
new file mode 100644
index 000000000..fe317282e
--- /dev/null
+++ b/sci-biology/ugene/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci</herd>
+	<maintainer>
+		<email>alexxy@gentoo.org</email>
+		<name>Alexey Shvetsov</name>
+	</maintainer>
+</pkgmetadata>
diff --git a/sci-biology/ugene/ugene-1.13.3.ebuild b/sci-biology/ugene/ugene-1.13.3.ebuild
new file mode 100644
index 000000000..af8c07067
--- /dev/null
+++ b/sci-biology/ugene/ugene-1.13.3.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit qt4-r2
+
+DESCRIPTION="A free open-source cross-platform bioinformatics software"
+HOMEPAGE="http://ugene.unipro.ru"
+SRC_URI="http://${PN}.unipro.ru/downloads/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="sse2"
+
+DEPEND="
+	dev-qt/qtgui:4"
+RDEPEND="${DEPEND}"
+
+LANGS="cs en ru zh"
+
+src_configure() {
+	local CONFIG_OPTS
+	if use amd64; then
+		CONFIG_OPTS+=( CONFIG+="x64" )
+	elif use ppc; then
+		CONFIG_OPTS+=( CONFIG+="ppc" )
+	fi
+
+	use sse2 && CONFIG_OPTS+=( use_sse2 )
+
+	eqmake4 $CONFIG_OPTS || die
+}