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commit: 18242e80e4a76451d4559ec3c788304525f34446 |
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Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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AuthorDate: Fri Aug 7 12:15:21 2020 +0000 |
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Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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CommitDate: Fri Aug 7 12:15:21 2020 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=18242e80 |
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|
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sci-biology/hisat2: version bump |
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|
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Package-Manager: Portage-2.3.100, Repoman-2.3.22 |
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Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz> |
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|
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...S.patch => hisat2-2.2.1-respect_CXXFLAGS.patch} | 22 +++++----------------- |
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.../{hisat2-2.0.5.ebuild => hisat2-2.2.1.ebuild} | 6 +++--- |
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2 files changed, 8 insertions(+), 20 deletions(-) |
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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/hisat2-2.2.1-respect_CXXFLAGS.patch |
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similarity index 61% |
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rename from sci-biology/hisat2/files/hisat2-2.0.5-respect_CXXFLAGS.patch |
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rename to sci-biology/hisat2/files/hisat2-2.2.1-respect_CXXFLAGS.patch |
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index 26db123c8..4ca550c66 100644 |
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--- a/sci-biology/hisat2/files/hisat2-2.0.5-respect_CXXFLAGS.patch |
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+++ b/sci-biology/hisat2/files/hisat2-2.2.1-respect_CXXFLAGS.patch |
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@@ -1,18 +1,6 @@ |
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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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+--- hisat2-2.2.1/Makefile.ori 2020-08-07 13:12:25.393396171 +0200 |
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++++ hisat2-2.2.1/Makefile 2020-08-07 13:15:56.845080223 +0200 |
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+@@ -152,30 +152,30 @@ |
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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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@@ -43,8 +31,8 @@ |
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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_FLAGS = -O0 -g3 $(BITS_FLAG) $(SSE_FLAG) |
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++DEBUG_FLAGS = -g3 -O0 $(CXXFLAGS) $(BITS_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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|
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diff --git a/sci-biology/hisat2/hisat2-2.0.5.ebuild b/sci-biology/hisat2/hisat2-2.2.1.ebuild |
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similarity index 89% |
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rename from sci-biology/hisat2/hisat2-2.0.5.ebuild |
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rename to sci-biology/hisat2/hisat2-2.2.1.ebuild |
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index d200a57ac..5532d2b71 100644 |
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--- a/sci-biology/hisat2/hisat2-2.0.5.ebuild |
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+++ b/sci-biology/hisat2/hisat2-2.2.1.ebuild |
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@@ -1,9 +1,9 @@ |
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-# Copyright 1999-2017 Gentoo Foundation |
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+# Copyright 1999-2020 Gentoo Authors |
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# Distributed under the terms of the GNU General Public License v2 |
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|
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EAPI=6 |
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|
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-PYTHON_COMPAT=( python2_7 ) |
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+PYTHON_COMPAT=( python3_{6,7,8} ) |
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|
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inherit python-r1 |
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|
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@@ -11,7 +11,7 @@ DESCRIPTION="Align DNA reads to a population of genomes" |
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HOMEPAGE=" |
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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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+SRC_URI="https://cloud.biohpc.swmed.edu/index.php/s/fE9QCsX3NH4QwBi/download -> ${P}.zip" |
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|
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LICENSE="GPL-3+" |
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SLOT="0" |
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