From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id 6078C138359 for ; Fri, 7 Aug 2020 12:15:31 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id A7ABBE0875; Fri, 7 Aug 2020 12:15:30 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 895C0E0875 for ; Fri, 7 Aug 2020 12:15:30 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 144B934F4A8 for ; Fri, 7 Aug 2020 12:15:29 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id C38E82FD for ; Fri, 7 Aug 2020 12:15:27 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <1596802521.18242e80e4a76451d4559ec3c788304525f34446.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/hisat2/files/, sci-biology/hisat2/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/hisat2/files/hisat2-2.0.5-respect_CXXFLAGS.patch sci-biology/hisat2/files/hisat2-2.2.1-respect_CXXFLAGS.patch sci-biology/hisat2/hisat2-2.0.5.ebuild sci-biology/hisat2/hisat2-2.2.1.ebuild X-VCS-Directories: sci-biology/hisat2/files/ sci-biology/hisat2/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 18242e80e4a76451d4559ec3c788304525f34446 X-VCS-Branch: master Date: Fri, 7 Aug 2020 12:15:27 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: f28c217b-748d-4750-8a05-7ad36eda0531 X-Archives-Hash: 3a7b8468031dc956f69bc92afddb5ce0 commit: 18242e80e4a76451d4559ec3c788304525f34446 Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Fri Aug 7 12:15:21 2020 +0000 Commit: Martin Mokrejs fold natur cuni 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 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"