commit: 18242e80e4a76451d4559ec3c788304525f34446
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Aug 7 12:15:21 2020 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Aug 7 12:15:21 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=18242e80
sci-biology/hisat2: version bump
Package-Manager: Portage-2.3.100, Repoman-2.3.22
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
...S.patch => hisat2-2.2.1-respect_CXXFLAGS.patch} | 22 +++++-----------------
.../{hisat2-2.0.5.ebuild => hisat2-2.2.1.ebuild} | 6 +++---
2 files changed, 8 insertions(+), 20 deletions(-)
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
similarity index 61%
rename from sci-biology/hisat2/files/hisat2-2.0.5-respect_CXXFLAGS.patch
rename to 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) $(SSE_FLAG) -funroll-loops
diff --git a/sci-biology/hisat2/hisat2-2.0.5.ebuild
b/sci-biology/hisat2/hisat2-2.2.1.ebuild
similarity index 89%
rename from sci-biology/hisat2/hisat2-2.0.5.ebuild
rename to sci-biology/hisat2/hisat2-2.2.1.ebuild
index d200a57ac..5532d2b71 100644
--- a/sci-biology/hisat2/hisat2-2.0.5.ebuild
+++ b/sci-biology/hisat2/hisat2-2.2.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
-PYTHON_COMPAT=( python2_7 )
+PYTHON_COMPAT=( python3_{6,7,8} )
inherit python-r1
@@ -11,7 +11,7 @@ DESCRIPTION="Align DNA reads to a population of genomes"
HOMEPAGE="
https://ccb.jhu.edu/software/hisat2
https://github.com/infphilo/hisat2";
-SRC_URI="ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/${P}-source.zip";
+SRC_URI="https://cloud.biohpc.swmed.edu/index.php/s/fE9QCsX3NH4QwBi/download
-> ${P}.zip"
LICENSE="GPL-3+"
SLOT="0"
