* [gentoo-commits] proj/sci:master commit in: sci-biology/brat/
@ 2013-12-09 8:33 Justin Lecher
0 siblings, 0 replies; 3+ messages in thread
From: Justin Lecher @ 2013-12-09 8:33 UTC (permalink / raw
To: gentoo-commits
commit: 6ee8d483c8788e331f785fe304231a7d93945f94
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Dec 6 09:37:28 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Dec 9 07:48:34 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6ee8d483
sci-biology/brat: Version Bump
Package-Manager: portage-2.2.7
---
sci-biology/brat/ChangeLog | 8 ++++++-
sci-biology/brat/brat-1.1.13.ebuild | 22 -------------------
sci-biology/brat/brat-1.2.4.ebuild | 43 +++++++++++++++++++++++++++++++++++++
sci-biology/brat/metadata.xml | 10 ++++-----
4 files changed, 55 insertions(+), 28 deletions(-)
diff --git a/sci-biology/brat/ChangeLog b/sci-biology/brat/ChangeLog
index 50b61de..ef720c7 100644
--- a/sci-biology/brat/ChangeLog
+++ b/sci-biology/brat/ChangeLog
@@ -1,7 +1,13 @@
# ChangeLog for sci-biology/brat
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*brat-1.2.4 (06 Dec 2013)
+
+ 06 Dec 2013; Justin Lecher <jlec@gentoo.org> -brat-1.1.13.ebuild,
+ +brat-1.2.4.ebuild, metadata.xml:
+ Version Bump
+
09 May 2010; Andrey Kislyuk <weaver@gentoo.org> ChangeLog:
New package, ebuild written by me
diff --git a/sci-biology/brat/brat-1.1.13.ebuild b/sci-biology/brat/brat-1.1.13.ebuild
deleted file mode 100644
index 649d1d9..0000000
--- a/sci-biology/brat/brat-1.1.13.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bfast/bfast-0.6.4c.ebuild,v 1.1 2010/05/07 19:21:57 weaver Exp $
-
-EAPI="2"
-
-DESCRIPTION="Bisulfite-treated Reads Analysis Tool"
-HOMEPAGE="http://compbio.cs.ucr.edu/brat/"
-SRC_URI="http://compbio.cs.ucr.edu/brat/downloads/brat-${PV}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-DEPEND=""
-RDEPEND=""
-
-src_install() {
- dobin brat brat-large acgt-count trim brat-large-build || die
- dodoc BRAT_USER_MANUAL_${PV//./_}.pdf || die
-}
diff --git a/sci-biology/brat/brat-1.2.4.ebuild b/sci-biology/brat/brat-1.2.4.ebuild
new file mode 100644
index 0000000..6e971a0
--- /dev/null
+++ b/sci-biology/brat/brat-1.2.4.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bfast/bfast-0.6.4c.ebuild,v 1.1 2010/05/07 19:21:57 weaver Exp $
+
+EAPI=5
+
+inherit toolchain-funcs
+
+DESCRIPTION="Bisulfite-treated Reads Analysis Tool"
+HOMEPAGE="http://compbio.cs.ucr.edu/brat/"
+SRC_URI="http://compbio.cs.ucr.edu/${PN}/downloads/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND=""
+
+src_prepare() {
+ sed \
+ -e "s:g++:$(tc-getCXX):g" \
+ -e "s:-O3:${CFLAGS} ${LDFLAGS}:g" \
+ -e "s:-w:-Wall:g" \
+ -i Makefile || die
+}
+
+src_test() {
+ cd test_quick_start || die
+ ebegin "unpacking test files"
+ tar xzf test_data.tgz || die
+ eend $?
+
+ ../brat -r references.txt -1 test_reads1.txt -2 test_reads2.txt -o output.txt -bs -pe -i 200 -a 300 || die
+ ../brat -r references.txt -s test_reads1.txt -o output_singles1.txt -bs || die
+ ../brat -r references.txt -s test_reads2.txt -o output_singles2.txt -bs -A || die
+}
+
+src_install() {
+ dobin ${PN} ${PN}-large trim acgt-count ${PN}-large-build rev-compl check-strands remove-dupl convert-to-sam
+ dodoc BRAT_USER_MANUAL_*.pdf
+}
diff --git a/sci-biology/brat/metadata.xml b/sci-biology/brat/metadata.xml
index 3302123..fc7c769 100644
--- a/sci-biology/brat/metadata.xml
+++ b/sci-biology/brat/metadata.xml
@@ -1,9 +1,9 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer>
- <email>weaver@gentoo.org</email>
- <name>Andrey Kislyuk</name>
- </maintainer>
- <herd>sci-biology</herd>
+ <maintainer>
+ <email>weaver@gentoo.org</email>
+ <name>Andrey Kislyuk</name>
+ </maintainer>
+ <herd>sci-biology</herd>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/brat/
@ 2016-09-01 9:07 Martin Mokrejs
0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2016-09-01 9:07 UTC (permalink / raw
To: gentoo-commits
commit: 95109ad272fdaef588147cef35dd1ed5bdced515
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Sep 1 09:07:42 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Sep 1 09:07:42 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=95109ad2
sci-biology/brat: polish DESCRIPTION
Package-Manager: portage-2.3.0
sci-biology/brat/brat-1.2.4.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/brat/brat-1.2.4.ebuild b/sci-biology/brat/brat-1.2.4.ebuild
index d7a5432..2652061 100644
--- a/sci-biology/brat/brat-1.2.4.ebuild
+++ b/sci-biology/brat/brat-1.2.4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -6,7 +6,7 @@ EAPI=5
inherit toolchain-funcs
-DESCRIPTION="Bisulfite-treated Reads Analysis Tool"
+DESCRIPTION="Bisulfite-treated Reads Analysis Tool (short read mapper)"
HOMEPAGE="http://compbio.cs.ucr.edu/brat/"
SRC_URI="http://compbio.cs.ucr.edu/${PN}/downloads/${P}.tar.gz"
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/brat/
@ 2021-03-06 10:07 Andrew Ammerlaan
0 siblings, 0 replies; 3+ messages in thread
From: Andrew Ammerlaan @ 2021-03-06 10:07 UTC (permalink / raw
To: gentoo-commits
commit: 47851791c55a26d03bdc92dd32542b399759161e
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar 6 10:04:58 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar 6 10:04:58 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=47851791
sci-biology/brat: EAPI bump
Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/brat/brat-1.2.4.ebuild | 9 +++------
1 file changed, 3 insertions(+), 6 deletions(-)
diff --git a/sci-biology/brat/brat-1.2.4.ebuild b/sci-biology/brat/brat-1.2.4.ebuild
index 39e29328d..2be8dcf0b 100644
--- a/sci-biology/brat/brat-1.2.4.ebuild
+++ b/sci-biology/brat/brat-1.2.4.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 +11,10 @@ SRC_URI="http://compbio.cs.ucr.edu/${PN}/downloads/${P}.tar.gz"
LICENSE="GPL-3"
SLOT="0"
-IUSE=""
KEYWORDS="~amd64 ~x86"
-DEPEND=""
-RDEPEND=""
-
src_prepare() {
+ default
sed \
-e "s:g++:$(tc-getCXX):g" \
-e "s:-O3:${CFLAGS} ${LDFLAGS}:g" \
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