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| author |   Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> | 2020-08-07 14:15:21 +0200 |
|---|---|---|
| committer | Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> | 2020-08-07 14:15:21 +0200 |
| commit | 18242e80e4a76451d4559ec3c788304525f34446 (patch) | |
| tree | f2bfb852d649f562a3d3b49897e389a807c92444 | |
| parent | sci-libs/pytorch: bump to 1.6.0. (diff) | |
| download | sci-18242e80e4a76451d4559ec3c788304525f34446.tar.gz sci-18242e80e4a76451d4559ec3c788304525f34446.tar.bz2 sci-18242e80e4a76451d4559ec3c788304525f34446.zip | |
sci-biology/hisat2: version bump
Package-Manager: Portage-2.3.100, Repoman-2.3.22
Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
| -rw-r--r-- | sci-biology/hisat2/Manifest | 2 | ||||
| -rw-r--r-- | sci-biology/hisat2/files/hisat2-2.2.1-respect_CXXFLAGS.patch (renamed from sci-biology/hisat2/files/hisat2-2.0.5-respect_CXXFLAGS.patch) | 22 | ||||
| -rw-r--r-- | sci-biology/hisat2/hisat2-2.2.1.ebuild (renamed from sci-biology/hisat2/hisat2-2.0.5.ebuild) | 6 |
3 files changed, 9 insertions, 21 deletions
diff --git a/sci-biology/hisat2/Manifest b/sci-biology/hisat2/Manifest index 70929dffa..226bc245a 100644 --- a/sci-biology/hisat2/Manifest +++ b/sci-biology/hisat2/Manifest @@ -1 +1 @@ -DIST hisat2-2.0.5-source.zip 3914703 BLAKE2B 3da01db5ea2acef3d9c8afd14f8efc93ee6c71f68d97b06e4a20e5ab72a7d39babf8dba9e74488aa3fc8a7062a0554b356d555703d49496de71248027ff76a6c SHA512 a626ebf8bb2682bdd69ffde55d1f53c6926ef6172a2d852aadc7fb02c08ab7b1b25158e046a6e07acb4f406549c37a329e5354402eaa5e93612568c7c58b2559 +DIST hisat2-2.2.1.zip 3926862 BLAKE2B d4155299d3973914dfb1b6fe85f7a1e9a438d87f9ddcc7d228d5c8d35f685871b44588e3f50fe023f3ef98b91929437c53f44424640a966e3561a264a3669878 SHA512 42d399073d947801bc7c3d2032a49a902fed59b09fa24aaef4ac6b72de6b1544238782604dbef3ace26b19d8ab722209df669ee871be94a0c589dd6c6acbe5af 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 index 26db123c8..4ca550c66 100644 --- a/sci-biology/hisat2/files/hisat2-2.0.5-respect_CXXFLAGS.patch +++ b/sci-biology/hisat2/files/hisat2-2.2.1-respect_CXXFLAGS.patch @@ -1,18 +1,6 @@ ---- hisat2-2.0.5/Makefile.ori 2017-03-01 11:35:36.430368298 +0100 -+++ hisat2-2.0.5/Makefile 2017-03-01 11:43:42.974034697 +0100 -@@ -23,9 +23,8 @@ - INC = - GCC_PREFIX = $(shell dirname `which gcc`) - GCC_SUFFIX = --CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX) --CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX) --CXX = $(CPP) -+CXX ?= $(GCC_PREFIX)/g++$(GCC_SUFFIX) -+CXXFLAGS ?= "-O3" - HEADERS = $(wildcard *.h) - BOWTIE_MM = 1 - BOWTIE_SHARED_MEM = 0 -@@ -134,30 +133,30 @@ +--- hisat2-2.2.1/Makefile.ori 2020-08-07 13:12:25.393396171 +0200 ++++ hisat2-2.2.1/Makefile 2020-08-07 13:15:56.845080223 +0200 +@@ -152,30 +152,30 @@ VERSION = $(shell cat VERSION) # Convert BITS=?? to a -m flag @@ -43,8 +31,8 @@ -SSE_FLAG=-msse2 +SSE_FLAG?=-msse2 --DEBUG_FLAGS = -O0 -g3 $(BIToS_FLAG) $(SSE_FLAG) -+DEBUG_FLAGS = -g3 -O0 $(CXXFLAGS) $(BIToS_FLAG) $(SSE_FLAG) +-DEBUG_FLAGS = -O0 -g3 $(BITS_FLAG) $(SSE_FLAG) ++DEBUG_FLAGS = -g3 -O0 $(CXXFLAGS) $(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) $(BITS_FLAG) $(SSE_FLAG) -funroll-loops diff --git a/sci-biology/hisat2/hisat2-2.0.5.ebuild b/sci-biology/hisat2/hisat2-2.2.1.ebuild index d200a57ac..5532d2b71 100644 --- a/sci-biology/hisat2/hisat2-2.0.5.ebuild +++ b/sci-biology/hisat2/hisat2-2.2.1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 -PYTHON_COMPAT=( python2_7 ) +PYTHON_COMPAT=( python3_{6,7,8} ) inherit python-r1 @@ -11,7 +11,7 @@ DESCRIPTION="Align DNA reads to a population of genomes" HOMEPAGE=" https://ccb.jhu.edu/software/hisat2 https://github.com/infphilo/hisat2" -SRC_URI="ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/${P}-source.zip" +SRC_URI="https://cloud.biohpc.swmed.edu/index.php/s/fE9QCsX3NH4QwBi/download -> ${P}.zip" LICENSE="GPL-3+" SLOT="0" |