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commit: 0765721b800e099f0e7d29d715fc39047d1b0f65 |
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Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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AuthorDate: Wed Mar 1 11:28:52 2017 +0000 |
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Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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CommitDate: Wed Mar 1 11:28:52 2017 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=0765721b |
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|
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sci-biology/hisat2: new package |
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|
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Package-Manager: Portage-2.3.3, Repoman-2.3.1 |
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|
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.../files/hisat2-2.0.5-respect_CXXFLAGS.patch | 53 ++++++++++++++++++++++ |
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sci-biology/hisat2/hisat2-2.0.5.ebuild | 51 +++++++++++++++++++++ |
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sci-biology/hisat2/metadata.xml | 12 +++++ |
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3 files changed, 116 insertions(+) |
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|
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diff --git a/sci-biology/hisat2/files/hisat2-2.0.5-respect_CXXFLAGS.patch b/sci-biology/hisat2/files/hisat2-2.0.5-respect_CXXFLAGS.patch |
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new file mode 100644 |
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index 000000000..26db123c8 |
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--- /dev/null |
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+++ b/sci-biology/hisat2/files/hisat2-2.0.5-respect_CXXFLAGS.patch |
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@@ -0,0 +1,53 @@ |
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+--- hisat2-2.0.5/Makefile.ori 2017-03-01 11:35:36.430368298 +0100 |
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++++ hisat2-2.0.5/Makefile 2017-03-01 11:43:42.974034697 +0100 |
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+@@ -23,9 +23,8 @@ |
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+ INC = |
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+ GCC_PREFIX = $(shell dirname `which gcc`) |
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+ GCC_SUFFIX = |
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+-CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX) |
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+-CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX) |
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+-CXX = $(CPP) |
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++CXX ?= $(GCC_PREFIX)/g++$(GCC_SUFFIX) |
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++CXXFLAGS ?= "-O3" |
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+ HEADERS = $(wildcard *.h) |
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+ BOWTIE_MM = 1 |
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+ BOWTIE_SHARED_MEM = 0 |
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+@@ -134,30 +133,30 @@ |
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+ VERSION = $(shell cat VERSION) |
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+ |
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+ # Convert BITS=?? to a -m flag |
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+-BITS=32 |
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++BITS?=32 |
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+ ifeq (x86_64,$(shell uname -m)) |
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+-BITS=64 |
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++BITS?=64 |
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+ endif |
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+ # msys will always be 32 bit so look at the cpu arch instead. |
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+ ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITEW6432))) |
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+ ifeq (1,$(MINGW)) |
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+- BITS=64 |
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++ BITS?=64 |
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+ endif |
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+ endif |
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+ BITS_FLAG = |
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+ |
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+ ifeq (32,$(BITS)) |
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+- BITS_FLAG = -m32 |
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++ BITS_FLAG ?= -m32 |
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+ endif |
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+ |
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+ ifeq (64,$(BITS)) |
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+- BITS_FLAG = -m64 |
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++ BITS_FLAG ?= -m64 |
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+ endif |
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+-SSE_FLAG=-msse2 |
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++SSE_FLAG?=-msse2 |
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+ |
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+-DEBUG_FLAGS = -O0 -g3 $(BIToS_FLAG) $(SSE_FLAG) |
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++DEBUG_FLAGS = -g3 -O0 $(CXXFLAGS) $(BIToS_FLAG) $(SSE_FLAG) |
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+ DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\"" |
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+-RELEASE_FLAGS = -O3 $(BITS_FLAG) $(SSE_FLAG) -funroll-loops -g3 |
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++RELEASE_FLAGS = $(CXXFLAGS) $(BITS_FLAG) $(SSE_FLAG) -funroll-loops |
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+ RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\"" |
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+ NOASSERT_FLAGS = -DNDEBUG |
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+ FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE |
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|
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diff --git a/sci-biology/hisat2/hisat2-2.0.5.ebuild b/sci-biology/hisat2/hisat2-2.0.5.ebuild |
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new file mode 100644 |
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index 000000000..a8a81a26f |
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--- /dev/null |
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+++ b/sci-biology/hisat2/hisat2-2.0.5.ebuild |
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@@ -0,0 +1,51 @@ |
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+# Copyright 1999-2017 Gentoo Foundation |
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+# Distributed under the terms of the GNU General Public License v2 |
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+# $Id$ |
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+ |
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+EAPI=6 |
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+ |
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+inherit eutils |
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+ |
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+DESCRIPTION="Align DNA reads to a population of genomes" |
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+HOMEPAGE="https://ccb.jhu.edu/software/hisat2 |
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+ https://github.com/infphilo/hisat2" |
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+SRC_URI="ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/${P}-source.zip" |
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+ |
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+LICENSE="GPL-3+" |
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+SLOT="0" |
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+KEYWORDS="~amd64 ~x86" |
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+IUSE="cpu_flags_x86_sse2" |
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+ |
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+DEPEND="" |
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+RDEPEND="${DEPEND}" |
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+ |
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+PATCHES=( "${FILESDIR}"/${P}-respect_CXXFLAGS.patch ) |
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+ |
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+# TODO: could depend on sci-biology/ncbi-tools++ or sra_sdk containing ncbi-vdb |
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+# For the support of SRA data access in HISAT2, please download and install the [NCBI-NGS] toolkit. |
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+# When running `make`, specify additional variables as follow. |
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+# `make USE_SRA=1 NCBI_NGS_DIR=/path/to/NCBI-NGS-directory NCBI_VDB_DIR=/path/to/NCBI-NGS-directory`, |
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+# where `NCBI_NGS_DIR` and `NCBI_VDB_DIR` will be used in Makefile for -I and -L compilation options. |
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+# For example, $(NCBI_NGS_DIR)/include and $(NCBI_NGS_DIR)/lib64 will be used. |
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+ |
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+src_configure(){ |
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+ if use cpu_flags_x86_sse2; then |
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+ SSE_FLAGS='-msse2' |
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+ fi |
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+ if [ "$ARCH" = "amd64" ] || [ "$ARCH" = "ia64" ] || [ "$ARCH" = "ppc64" ]; then |
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+ BITS='-m64' |
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+ else |
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+ BITS='-32' |
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+ fi |
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+} |
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+ |
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+src_compile(){ |
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+ emake SSE_FLAG="${SSE_FLAGS}" BITS="${BITS}" |
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+} |
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+ |
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+src_install(){ |
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+ dobin hisat2 hisat2-build hisat2-inspect hisat2-build-s hisat2-build-l hisat2-align-s hisat2-align-l hisat2-inspect-s hisat2-inspect-l *.py |
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+ insinto /usr/share/"${PN}"/scripts |
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+ doins scripts/*.sh |
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+ dodoc MANUAL TUTORIAL |
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+} |
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|
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diff --git a/sci-biology/hisat2/metadata.xml b/sci-biology/hisat2/metadata.xml |
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new file mode 100644 |
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index 000000000..f68a1b6fa |
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--- /dev/null |
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+++ b/sci-biology/hisat2/metadata.xml |
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@@ -0,0 +1,12 @@ |
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+<?xml version="1.0" encoding="UTF-8"?> |
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+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
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+<pkgmetadata> |
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+ <maintainer type="person"> |
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+ <email>mmokrejs@×××××××××××××××.cz</email> |
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+ <name>Martin Mokrejs</name> |
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+ </maintainer> |
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+ <maintainer type="project"> |
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+ <email>sci-biology@g.o</email> |
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+ <name>Gentoo Biology Project</name> |
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+ </maintainer> |
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+</pkgmetadata> |