commit: f72d427f9d61ba0b6d38fccd42edf1b041175191
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 12:28:04 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 12:28:14 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f72d427f
sci-biology/kraken: version bump, EAPI bump, use https
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
profiles/package.mask | 1 -
.../{kraken-1.0.ebuild => kraken-1.1.1.ebuild} | 21 +++++++++++----------
2 files changed, 11 insertions(+), 11 deletions(-)
diff --git a/profiles/package.mask b/profiles/package.mask
index e463a1e15..e1ef30102 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -76,4 +76,3 @@ sci-biology/jtreeview
sci-biology/jtreeview-bin
sci-biology/kat
sci-biology/KING
-sci-biology/kraken
diff --git a/sci-biology/kraken/kraken-1.0.ebuild
b/sci-biology/kraken/kraken-1.1.1.ebuild
similarity index 72%
rename from sci-biology/kraken/kraken-1.0.ebuild
rename to sci-biology/kraken/kraken-1.1.1.ebuild
index 2a021a329..47ca1b86e 100644
--- a/sci-biology/kraken/kraken-1.0.ebuild
+++ b/sci-biology/kraken/kraken-1.1.1.ebuild
@@ -1,29 +1,30 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
-PERL_EXPORT_PHASE_FUNCTIONS=no
inherit perl-module
DESCRIPTION="Detect sequencing project contaminants by mapping reads to
taxonomic groups"
-HOMEPAGE="http://ccb.jhu.edu/software/kraken
- https://genomebiology.com/2014/15/3/R46";
+HOMEPAGE="https://ccb.jhu.edu/software/kraken";
SRC_URI="https://github.com/DerrickWood/kraken/archive/v1.0.tar.gz ->
${P}.tar.gz
- http://ccb.jhu.edu/software/kraken/MANUAL.html -> ${P}_MANUAL.html"
+ https://ccb.jhu.edu/software/kraken/MANUAL.html -> ${P}_MANUAL.html"
LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64"
-IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
dev-lang/perl
net-misc/wget
- sci-biology/jellyfish:1"
+ sci-biology/jellyfish:1
+"
+
+S="${WORKDIR}/${PN}-1.0"
src_prepare(){
+ default
sed -e 's/^CXX = /CXX ?= /' -e 's/^CXXFLAGS = /CXXFLAGS ?= /' -i
src/Makefile || die
echo "exit 0" >> install_kraken.sh || die
}
@@ -47,7 +48,7 @@ src_install(){
pkg_postinst(){
ewarn "Kraken may optionally need <=sci-biology/jellyfish-2 if you want
to build your own dbs"
ewarn "Kraken needs high network bandwidth for its huge downloads, be
sure to read"
- ewarn "http://ccb.jhu.edu/software/kraken and prepare at least 160GB of
disk space"
+ ewarn "https://ccb.jhu.edu/software/kraken and prepare at least 160GB
of disk space"
ewarn "Consider placing the db files in ramfs (needs root permissions)
taking >75GB RAM"
- ewarn "Results can be visualized with
http://sourceforge.net/p/krona/home/krona";
+ ewarn "Results can be visualized with
https://sourceforge.net/p/krona/home/krona";
}
