diff options
| -rw-r--r-- | sci-biology/cd-hit/ChangeLog | 10 | ||||
| -rw-r--r-- | sci-biology/cd-hit/Manifest | 15 | ||||
| -rw-r--r-- | sci-biology/cd-hit/cd-hit-4.5.1.ebuild | 44 | ||||
| -rw-r--r-- | sci-biology/cd-hit/files/4.5.1-gentoo.patch | 85 | ||||
| -rw-r--r-- | sci-biology/cd-hit/metadata.xml | 24 |
5 files changed, 178 insertions, 0 deletions
diff --git a/sci-biology/cd-hit/ChangeLog b/sci-biology/cd-hit/ChangeLog new file mode 100644 index 000000000000..4d17282cd697 --- /dev/null +++ b/sci-biology/cd-hit/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/cd-hit +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/cd-hit/ChangeLog,v 1.1 2011/02/01 09:06:35 jlec Exp $ + +*cd-hit-4.5.1 (01 Feb 2011) + + 01 Feb 2011; Justin Lecher <jlec@gentoo.org> +files/4.5.1-gentoo.patch, + +cd-hit-4.5.1.ebuild, +metadata.xml: + New addition, written by me + diff --git a/sci-biology/cd-hit/Manifest b/sci-biology/cd-hit/Manifest new file mode 100644 index 000000000000..c3b5c4ff2dae --- /dev/null +++ b/sci-biology/cd-hit/Manifest @@ -0,0 +1,15 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + +AUX 4.5.1-gentoo.patch 2651 RMD160 71063f7be6ba64fd1884a9a4b60a2d625b86a70b SHA1 da89f23f35304095cb8f8db8ea3ddb65640738f5 SHA256 6582f6138bac7d29956a4284e60139ae04c30db7fc635df97ce792324b0d96fe +DIST cd-hit-v4.5.1-2011-01-31.tgz 368740 RMD160 118a37f44795db666cb9c6b53a5d29f4e72b73cb SHA1 5cd6e51390a7cee860fe97a51480d28f49bdcf61 SHA256 c1c3a3a772fc683fec3ff1763fdeec62a0a2a3925124f7a723fe3b271da35281 +EBUILD cd-hit-4.5.1.ebuild 1056 RMD160 58fda4827f77dd272ba0f72b264c26c9f2cb71c4 SHA1 9013bbdaf2d1e285eed4f63ade62bd71280b61a8 SHA256 6e73d3a504e0fd85786e36c2159fbfc651602bad2e0d43597e853f664b8bfa5b +MISC ChangeLog 380 RMD160 cec5a6af887f75aa6525a01b2b91cf4f7e6a0b3e SHA1 988acaa3de1a3d921afb4e3f7962632dea249dd8 SHA256 3b97199e55f0f4ba0b36706fc36afa3ee0a4e71f0d107961f11c2ec13c5de2a7 +MISC metadata.xml 1182 RMD160 fc96205490f768c92e7f3f846587a7900cb280e5 SHA1 1a23c6f28d8c27bf566681dbbfddfb80e925f068 SHA256 11b0329e729a4b0de427a402c47ce7d85b596e87c7296799c4fbad23a70cf558 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.16 (GNU/Linux) + +iEYEARECAAYFAk1HzSAACgkQgAnW8HDreRboDACePn+O5UTNY+lo2lU/uYDS7+MP +c58AnR3Bk8KwKpE1MbtgBcAT9R6wIe1t +=9vbS +-----END PGP SIGNATURE----- diff --git a/sci-biology/cd-hit/cd-hit-4.5.1.ebuild b/sci-biology/cd-hit/cd-hit-4.5.1.ebuild new file mode 100644 index 000000000000..16119f159316 --- /dev/null +++ b/sci-biology/cd-hit/cd-hit-4.5.1.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/cd-hit/cd-hit-4.5.1.ebuild,v 1.1 2011/02/01 09:06:35 jlec Exp $ + +EAPI="3" + +inherit flag-o-matic toolchain-funcs + +RELDATE="2011-01-31" +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="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() { + if use openmp; then + emake openmp=yes || die + else + emake || die + fi +} + +src_install() { + dobin cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div *.pl || die + dodoc ChangeLog cdhit-user-guide.pdf || die +} diff --git a/sci-biology/cd-hit/files/4.5.1-gentoo.patch b/sci-biology/cd-hit/files/4.5.1-gentoo.patch new file mode 100644 index 000000000000..c3eaf79cc8f2 --- /dev/null +++ b/sci-biology/cd-hit/files/4.5.1-gentoo.patch @@ -0,0 +1,85 @@ +diff --git a/Makefile b/Makefile +index f1eaa26..92d3130 100644 +--- a/Makefile ++++ b/Makefile +@@ -10,7 +10,7 @@ CCFLAGS = -O2 -DNO_OPENMP + # in command line: + # make openmp=yes + ifeq ($(openmp),yes) +-CCFLAGS = -O2 -fopenmp ++CXXFLAGS += -fopenmp + endif + + # support debugging +@@ -18,16 +18,16 @@ endif + # make debug=yes + # make openmp=yes debug=yes + ifeq ($(debug),yes) +-CCFLAGS += -ggdb ++CXXFLAGS += -ggdb + endif + + #LDFLAGS = -static -o +-LDFLAGS = -o ++LDFLAGS += -o + + PROGS = cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div + + .c++.o: +- $(CC) $(CCFLAGS) -c $< ++ $(CXX) $(CXXFLAGS) -c $< + + all: $(PROGS) + +@@ -37,39 +37,39 @@ clean: + # 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) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) 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) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) 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) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) 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) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) 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) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div + + # 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 + diff --git a/sci-biology/cd-hit/metadata.xml b/sci-biology/cd-hit/metadata.xml new file mode 100644 index 000000000000..0066dc245f77 --- /dev/null +++ b/sci-biology/cd-hit/metadata.xml @@ -0,0 +1,24 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci-biology</herd> +<maintainer> + <email>jlec@gentoo.org</email> +</maintainer> +<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> +</pkgmetadata> |