From e506aabb717f6536e683c88a998e7b566aab8164 Mon Sep 17 00:00:00 2001
From: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Mon, 8 Jan 2018 15:11:10 +0100
Subject: sci-biology/BRAKER: version bump

Package-Manager: Portage-2.3.19, Repoman-2.3.6
---
 sci-biology/BRAKER/BRAKER-1.9.ebuild | 51 ------------------------------------
 sci-biology/BRAKER/BRAKER-2.ebuild   | 51 ++++++++++++++++++++++++++++++++++++
 sci-biology/BRAKER/Manifest          |  2 +-
 3 files changed, 52 insertions(+), 52 deletions(-)
 delete mode 100644 sci-biology/BRAKER/BRAKER-1.9.ebuild
 create mode 100644 sci-biology/BRAKER/BRAKER-2.ebuild

diff --git a/sci-biology/BRAKER/BRAKER-1.9.ebuild b/sci-biology/BRAKER/BRAKER-1.9.ebuild
deleted file mode 100644
index 7c814763f..000000000
--- a/sci-biology/BRAKER/BRAKER-1.9.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module
-
-DESCRIPTION="Gene prediction based on RNA-Seq using GeneMark-ET and AUGUSTUS"
-# http://bioinf.uni-greifswald.de/bioinf/publications/pag2015.pdf
-HOMEPAGE="http://bioinf.uni-greifswald.de/bioinf/braker
-	http://bioinf.uni-greifswald.de/augustus/downloads"
-SRC_URI=" http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER1_v"${PV}".tar.gz -> ${P}.tar.gz"
-# Download BRAKER1 from http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER1.tar.gz.
-# The most recent release is version 1.8, from December 15th 2015.
-# Example data for testing the BRAKER1 pipeline is available at
-# http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER1examples.tar.gz (1.1 GB).
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-	dev-perl/Scalar-Util-Numeric
-	sci-biology/augustus"
-	#>=sci-biology/GeneMark_ET-bin-4.29"
-#
-# BUG:
-# this causes:
-# [blocks B      ] <perl-core/Scalar-List-Utils-1.380.0 ("<perl-core/Scalar-List-Utils-1.380.0" is blocking virtual/perl-Scalar-List-Utils-1.380.0)
-
-S="${WORKDIR}"/BRAKER_v"${PV}"
-
-src_prepare(){
-	sed -e 's/^use helpMod/use BRAKER::helpMod/' -i braker.pl || die
-}
-
-src_install(){
-	perl_set_version
-	dobin *.pl
-	insinto ${VENDOR_LIB}/${PN}
-	doins *.pm
-	dodoc README.braker
-}
-
-pkg_postinst(){
-	einfo "Please install sci-biology/GeneMark_ET after obtaininig a license and binaries from"
-	einfo "http://exon.gatech.edu/GeneMark/gmes_instructions.html"
-}
diff --git a/sci-biology/BRAKER/BRAKER-2.ebuild b/sci-biology/BRAKER/BRAKER-2.ebuild
new file mode 100644
index 000000000..b4c752457
--- /dev/null
+++ b/sci-biology/BRAKER/BRAKER-2.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+PERL_EXPORT_PHASE_FUNCTIONS=no
+inherit perl-module
+
+DESCRIPTION="Gene prediction based on RNA-Seq using GeneMark-ET and AUGUSTUS"
+# http://bioinf.uni-greifswald.de/bioinf/publications/pag2015.pdf
+HOMEPAGE="http://bioinf.uni-greifswald.de/bioinf/braker
+	http://bioinf.uni-greifswald.de/augustus/downloads"
+SRC_URI="http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER"${PV}".tar.gz -> ${P}.tar.gz"
+# Download BRAKER1 from http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER1.tar.gz.
+# The most recent release is version 1.8, from December 15th 2015.
+# Example data for testing the BRAKER1 pipeline is available at
+# http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER1examples.tar.gz (1.1 GB).
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+	dev-perl/Scalar-Util-Numeric
+	sci-biology/augustus"
+	#>=sci-biology/GeneMark_ET-bin-4.29"
+#
+# BUG:
+# this causes:
+# [blocks B      ] <perl-core/Scalar-List-Utils-1.380.0 ("<perl-core/Scalar-List-Utils-1.380.0" is blocking virtual/perl-Scalar-List-Utils-1.380.0)
+
+S="${WORKDIR}"/BRAKER_v"${PV}".0
+
+src_prepare(){
+	sed -e 's/^use helpMod/use BRAKER::helpMod/' -i braker.pl || die
+}
+
+src_install(){
+	perl_set_version
+	dobin *.pl
+	insinto ${VENDOR_LIB}/${PN}
+	doins *.pm
+	dodoc README.braker
+}
+
+pkg_postinst(){
+	einfo "Please install sci-biology/GeneMark_ET after obtaininig a license and binaries from"
+	einfo "http://exon.gatech.edu/GeneMark/gmes_instructions.html"
+}
diff --git a/sci-biology/BRAKER/Manifest b/sci-biology/BRAKER/Manifest
index 2e35a5331..e2c4ea415 100644
--- a/sci-biology/BRAKER/Manifest
+++ b/sci-biology/BRAKER/Manifest
@@ -1 +1 @@
-DIST BRAKER-1.9.tar.gz 32183 SHA256 41151efadba460b370c1a974d02f9db0d6d4d0d4dd69b0badb574cb085192275 SHA512 25603ce53ffa68d02cda3bee6c8438322d42f3987f5c6f98fcd9ba85b54b361ba11e3aad6ec0ec50493d90f5b3d726c2a475117be95aa01dd7b123769d5d8338 WHIRLPOOL 79d3f8a6e14e2d5848585f90490778ae5106dde123556f95cbc2161b0f51ef15d8781828f524b3ccf4b6f96b4d265817093ccf36a6d8f289e24b278d2c5955a7
+DIST BRAKER-2.tar.gz 56198 BLAKE2B 7433cfde0c0fd6b7335061d8cfb90e1e17d9a258b60ca0b88f2b222216566e11834129e3db9df85043137975b12343c4b4c2e9e835c3abf43d36af8075488f07 SHA512 67da52604a7269a45128bc2a226a3103d89ff3737aaf0126e231b3af3bc2d94f590927d58b1de03caf8d962f3691270c93be5d60d56f393f8bfd70c196b4bb02
-- 
cgit v1.2.3-65-gdbad