[gentoo-commits] proj/sci:master commit in: sci-biology/brat_bw/

[gentoo-commits] proj/sci:master commit in: sci-biology/brat_bw/

[Martin Mokrejs]

commit:     541abbcdf09e9575c2e021f5261e29b0a76a0327
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Sep  1 09:52:01 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Sep  1 09:52:01 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=541abbcd

sci-biology/brat_bw: new package, successor of sci-biology/brat

Package-Manager: portage-2.3.0

 sci-biology/brat_bw/brat_bw-2.0.1.ebuild | 36 ++++++++++++++++++++++++++++++++
 sci-biology/brat_bw/metadata.xml         |  8 +++++++
 2 files changed, 44 insertions(+)

diff --git a/sci-biology/brat_bw/brat_bw-2.0.1.ebuild b/sci-biology/brat_bw/brat_bw-2.0.1.ebuild
new file mode 100644
index 0000000..5060439
--- /dev/null
+++ b/sci-biology/brat_bw/brat_bw-2.0.1.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit toolchain-funcs
+
+DESCRIPTION="Bisulfite-aware short read mapper, FM-index, no InDel support"
+HOMEPAGE="http://compbio.cs.ucr.edu/brat/"
+SRC_URI="http://compbio.cs.ucr.edu/brat/downloads/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND="!sci-biology/brat"
+
+src_prepare() {
+	sed \
+		-e "s:-Wl,-O1 : :g" \
+		-e "s:g++:$(tc-getCXX):g" \
+		-e "s:-O3:${CFLAGS} ${LDFLAGS}:g" \
+		-e "s:-w:-Wall:g" \
+		-i Makefile || die
+}
+
+src_install() {
+	dobin brat_bw build_bw trim acgt-count remove-dupl convert_to_sam
+	# possible FILLE_COLLISION with sci-biology/brat (probably some binaries just do the same)
+	# dobin ${PN} ${PN}-large trim acgt-count ${PN}-large-build rev-compl check-strands remove-dupl convert-to-sam
+	dodoc README
+	newdoc {'User Manual BRAT_2_0_1.pdf','User_Manual_BRAT_2_0_1.pdf'}
+}

diff --git a/sci-biology/brat_bw/metadata.xml b/sci-biology/brat_bw/metadata.xml
new file mode 100644
index 0000000..004c995
--- /dev/null
+++ b/sci-biology/brat_bw/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+  </pkgmetadata>

[gentoo-commits] proj/sci:master commit in: sci-biology/brat_bw/

[Andrew Ammerlaan]

commit:     cb81b17a770b31df2c937149481a33e9b85eb7a0
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar  6 10:06:05 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar  6 10:06:05 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=cb81b17a

sci-biology/brat_bw: EAPI bump

Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/brat_bw/brat_bw-2.0.1.ebuild | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/sci-biology/brat_bw/brat_bw-2.0.1.ebuild b/sci-biology/brat_bw/brat_bw-2.0.1.ebuild
index 6ffdaa7c0..d6daf3d1f 100644
--- a/sci-biology/brat_bw/brat_bw-2.0.1.ebuild
+++ b/sci-biology/brat_bw/brat_bw-2.0.1.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 inherit toolchain-funcs
 
@@ -11,13 +11,13 @@ SRC_URI="http://compbio.cs.ucr.edu/brat/downloads/${P}.tar.gz"
 
 LICENSE="GPL-3"
 SLOT="0"
-IUSE=""
 KEYWORDS="~amd64 ~x86"
 
 DEPEND=""
 RDEPEND="!sci-biology/brat"
 
 src_prepare() {
+	default
 	sed \
 		-e "s:-Wl,-O1 : :g" \
 		-e "s:g++:$(tc-getCXX):g" \