diff options
| -rw-r--r-- | sci-biology/bowtie/Manifest | 4 | ||||
| -rw-r--r-- | sci-biology/bowtie/bowtie-2.1.0.ebuild | 61 | ||||
| -rw-r--r-- | sci-biology/bowtie/files/bowtie-2.1.0-buildsystem.patch | 20 | ||||
| -rw-r--r-- | sci-biology/bowtie/metadata.xml | 5 |
4 files changed, 90 insertions, 0 deletions
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest new file mode 100644 index 000000000..a441c96d8 --- /dev/null +++ b/sci-biology/bowtie/Manifest @@ -0,0 +1,4 @@ +AUX bowtie-2.1.0-buildsystem.patch 734 SHA256 8cc4d242c2b61a34503bc5f82a8baaa16c50b743751162060cefb9a3a3234587 SHA512 1d1f61e331874acb9503c4002c45b49f58145b3d7fb0e03245029e88f2783eb0ba01a6b47c1238d7c6fb82e9a3d7e103808f957151d79208b889f4a212d424f8 WHIRLPOOL e53d25c40781cb8eaffbd6990e2da6aaf44f56cf96caea7d89db17db55a48546f5308d682593a24b3a421a97d830dd21c047da9eb82138da29e1a7318319f2ab +DIST bowtie-2.1.0-source.zip 5697131 SHA256 90a9d3a6bd19ddc3a8f90b935c6a2288478572de2ad4039b29f91016b95ef4b0 SHA512 47535c0539674d81dfac16bf0f0730c766afce93fa91bef7eb4f73df2b73fb7988bc344495a909f81374a60ec79117b141442ff13a61af96fe4043dc0e47cc7c WHIRLPOOL fca873eb10c514c22e2aa46cce685050234c9d2838b7a66c6d5648425b980d93a627c187f26af16e74c6b70e8addb8c267dab5af68023b65591f8ad2616344fa +EBUILD bowtie-2.1.0.ebuild 1213 SHA256 f9755689df887af0c63c3821dbdf22a737f1d3b0519f28700f2643b52b7b7297 SHA512 5f05a0417e9be44afbf7936d60c8312abe9494a55fc7cac82c5a09c8a6cd2de99d2a615db7aac4d4e81c4f4f7180fe34dabd950d623ddbfe4aa107aeecbf48c3 WHIRLPOOL 4377327390df0633335738ad15b643660d4244bbd4638b46f8f90450ae0c59d4f227b60adf44c0c33954752e56cb61763fdce073b726d7b66f80446f9fe1da7f +MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3 diff --git a/sci-biology/bowtie/bowtie-2.1.0.ebuild b/sci-biology/bowtie/bowtie-2.1.0.ebuild new file mode 100644 index 000000000..c2c502442 --- /dev/null +++ b/sci-biology/bowtie/bowtie-2.1.0.ebuild @@ -0,0 +1,61 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils flag-o-matic toolchain-funcs + +DESCRIPTION="An ultrafast memory-efficient short read aligner" +HOMEPAGE="http://bowtie-bio.sourceforge.net/" +SRC_URI="mirror://sourceforge/bowtie-bio/${P}-source.zip" + +LICENSE="GPL-3" +SLOT="2" +IUSE="sse2 examples" +KEYWORDS="~amd64 ~x86" + +CDEPEND="dev-lang/perl" +DEPEND="${CDEPEND} \ + app-arch/unzip" +RDEPEND="${CDEPEND}" + +S="${WORKDIR}/${PN}2-${PV}" + +pkg_pretend() { + if ! use sse2 ; then + ebegin + eerror "bowtie2 requires sse2 support. Please make sure your system supports" + eerror "sse2 and enable the sse2 use flag." + eend + die + fi +} + +src_prepare() { + epatch "${FILESDIR}/${P}-buildsystem.patch" +} + +src_compile() { + use sse2 && append-cxxflags -msse2 + emake \ + CC="$(tc-getCC)" \ + CPP="$(tc-getCXX)" \ + EXTRA_FLAGS="${LDFLAGS}" \ + RELEASE_FLAGS="${CXXFLAGS}" +} + +src_install() { + dobin bowtie2 bowtie2-* + exeinto /usr/share/${PN}2/scripts + doexe scripts/* + + newman MANUAL bowtie2.1 + dodoc AUTHORS NEWS TUTORIAL + dohtml doc/manual.html doc/style.css + + if use examples; then + insinto /usr/share/${PN}2 + doins -r example + fi +} diff --git a/sci-biology/bowtie/files/bowtie-2.1.0-buildsystem.patch b/sci-biology/bowtie/files/bowtie-2.1.0-buildsystem.patch new file mode 100644 index 000000000..97300b1b0 --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-2.1.0-buildsystem.patch @@ -0,0 +1,20 @@ +--- Makefile.old 2013-09-22 12:07:12.606844000 +0200 ++++ Makefile 2013-09-22 13:06:03.113888200 +0200 +@@ -24,8 +24,6 @@ + INC = + GCC_PREFIX = $(shell dirname `which gcc`) + GCC_SUFFIX = +-CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX) +-CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX) + CXX = $(CPP) + HEADERS = $(wildcard *.h) + BOWTIE_MM = 1 +@@ -141,7 +139,7 @@ + + DEBUG_FLAGS = -O0 -g3 $(BITS_FLAG) $(SSE_FLAG) + DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\"" +-RELEASE_FLAGS = -O3 $(BITS_FLAG) $(SSE_FLAG) -funroll-loops -g3 ++RELEASE_FLAGS = $(CXXFLAGS) + RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\"" + NOASSERT_FLAGS = -DNDEBUG + FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE diff --git a/sci-biology/bowtie/metadata.xml b/sci-biology/bowtie/metadata.xml new file mode 100644 index 000000000..f17a827e3 --- /dev/null +++ b/sci-biology/bowtie/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> |