commit: a0e0a0d9d53e45889552358f44d6efe8f43bcec9
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 09:22:34 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 09:22:47 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a0e0a0d9
sci-biology/SnpEff: fix fetching
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
profiles/package.mask | 1 -
.../SnpEff/{SnpEff-4.3i.ebuild => SnpEff-4.3t.ebuild} | 17 +++++------------
2 files changed, 5 insertions(+), 13 deletions(-)
diff --git a/profiles/package.mask b/profiles/package.mask
index 9232daefe..75f194351 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -102,4 +102,3 @@ sci-biology/scaffold_builder
sci-biology/sgp2
sci-biology/skewer-bin
sci-biology/smalt
-sci-biology/SnpEff
diff --git a/sci-biology/SnpEff/SnpEff-4.3i.ebuild
b/sci-biology/SnpEff/SnpEff-4.3t.ebuild
similarity index 86%
rename from sci-biology/SnpEff/SnpEff-4.3i.ebuild
rename to sci-biology/SnpEff/SnpEff-4.3t.ebuild
index 2bd2bfb1d..ddece0256 100644
--- a/sci-biology/SnpEff/SnpEff-4.3i.ebuild
+++ b/sci-biology/SnpEff/SnpEff-4.3t.ebuild
@@ -1,24 +1,20 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
inherit java-pkg-2 java-ant-2
-MY_PV=${PV/./_}
-
DESCRIPTION="SnpEff, SnpSift: Annotate SNP changes and predict effect in
HGVS-compliant VCF"
HOMEPAGE="https://pcingola.github.io/SnpEff/";
SRC_URI="
- https://sourceforge.net/projects/snpeff/files/snpEff_v${MY_PV}_core.zip
+
https://downloads.sourceforge.net/project/snpeff/snpEff_v${PV//./_}_core.zip
https://pcingola.github.io/SnpEff/index.html -> ${P}.html"
LICENSE="LGPL-3"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
+KEYWORDS=""
-# https://github.com/pcingola/SnpEff/blob/master/README_release.txt
RDEPEND="
>=virtual/jre-1.7:*
dev-java/maven-bin:*
@@ -26,13 +22,10 @@ RDEPEND="
DEPEND="${RDEPEND}
>=virtual/jdk-1.7:*
dev-java/ant-core"
+BDEPEND="app-arch/unzip"
S="${WORKDIR}"
-#src_compile(){
-# mvn || die
-#}
-
src_install(){
cd .. || die
mkdir -p "${ED}"/usr/share || die
