commit: 93af8540f3b3eb5fa7f0219cbb9d2eb8f1ec2e4d
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Fri Mar 5 15:48:10 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Fri Mar 5 15:48:10 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=93af8540
sci-biology/Rcorrector: bump 1.0.4, EAPI bump, add keywords
Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
.../{Rcorrector-9999.ebuild => Rcorrector-1.0.4.ebuild} | 17 ++++++++---------
.../Rcorrector/files/Rcorrector-rename-jellyfish.patch | 8 ++++----
2 files changed, 12 insertions(+), 13 deletions(-)
diff --git a/sci-biology/Rcorrector/Rcorrector-9999.ebuild
b/sci-biology/Rcorrector/Rcorrector-1.0.4.ebuild
similarity index 74%
rename from sci-biology/Rcorrector/Rcorrector-9999.ebuild
rename to sci-biology/Rcorrector/Rcorrector-1.0.4.ebuild
index 58007a73b..7522e86d3 100644
--- a/sci-biology/Rcorrector/Rcorrector-9999.ebuild
+++ b/sci-biology/Rcorrector/Rcorrector-1.0.4.ebuild
@@ -1,27 +1,26 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
-
-inherit git-r3 eutils
+EAPI=7
DESCRIPTION="Error correction for Illumina RNA-seq reads"
HOMEPAGE="https://github.com/mourisl/Rcorrector";
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/mourisl/Rcorrector.git";
+SRC_URI="https://github.com/mourisl/Rcorrector/archive/v${PV}.tar.gz ->
${P}.tar.gz"
LICENSE="GPL-2+"
SLOT="0"
-KEYWORDS=""
-IUSE=""
+KEYWORDS="~amd64"
DEPEND=">=sci-biology/jellyfish-2.1.3:2"
RDEPEND="${DEPEND}
dev-lang/perl"
+PATCHES=(
+ "${FILESDIR}"/Rcorrector-rename-jellyfish.patch
+)
+
src_prepare(){
default
- epatch "${FILESDIR}"/Rcorrector-rename-jellyfish.patch
# prevent building of jellyfish from bundled sources
mkdir -p ./jellyfish/bin/ || die
touch ./jellyfish/bin/jellyfish2 || die
diff --git a/sci-biology/Rcorrector/files/Rcorrector-rename-jellyfish.patch
b/sci-biology/Rcorrector/files/Rcorrector-rename-jellyfish.patch
index 08b9918d4..12962e124 100644
--- a/sci-biology/Rcorrector/files/Rcorrector-rename-jellyfish.patch
+++ b/sci-biology/Rcorrector/files/Rcorrector-rename-jellyfish.patch
@@ -1,5 +1,5 @@
---- Makefile.ori 2018-04-21 17:47:38.017147315 +0200
-+++ Makefile 2018-04-21 17:48:29.038679685 +0200
+--- a/Makefile 2018-04-21 17:47:38.017147315 +0200
++++ b/Makefile 2018-04-21 17:48:29.038679685 +0200
@@ -2,14 +2,14 @@
CXXFLAGS= -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize
-std=c++0x
LINKFLAGS = -I . -lpthread -lz
@@ -18,8 +18,8 @@
then \
wget -O jellyfish.tar.gz
https://github.com/gmarcais/Jellyfish/releases/download/v2.2.4/jellyfish-2.2.4.tar.gz
;\
tar -xzf jellyfish.tar.gz ; mv jellyfish-2.2.4
jellyfish ; rm jellyfish.tar.gz ; cd jellyfish && ./configure && make ;\
---- run_rcorrector.pl.ori 2018-04-21 17:48:43.459112787 +0200
-+++ run_rcorrector.pl 2018-04-21 17:49:18.070152287 +0200
+--- a/run_rcorrector.pl 2018-04-21 17:48:43.459112787 +0200
++++ b/run_rcorrector.pl 2018-04-21 17:49:18.070152287 +0200
@@ -42,10 +42,10 @@
die "$usage\n" ;
}
