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

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

[Martin Mokrejs]

commit:     178526185526bc8e42c47646d3d00af81072a31d
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Sep  1 10:05:22 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Sep  1 10:05:22 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=17852618

sci-biology/brat_nova: yet another rewrite of sci-biology/brat and brat_bw

Package-Manager: portage-2.3.0

 sci-biology/brat_nova/brat_nova-20160103.ebuild | 38 +++++++++++++++++++++++++
 sci-biology/brat_nova/metadata.xml              |  8 ++++++
 2 files changed, 46 insertions(+)

diff --git a/sci-biology/brat_nova/brat_nova-20160103.ebuild b/sci-biology/brat_nova/brat_nova-20160103.ebuild
new file mode 100644
index 0000000..3a3fa2b
--- /dev/null
+++ b/sci-biology/brat_nova/brat_nova-20160103.ebuild
@@ -0,0 +1,38 @@
+# 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 (improved brat_bw)"
+HOMEPAGE="http://compbio.cs.ucr.edu/brat/"
+SRC_URI="http://compbio.cs.ucr.edu/brat/downloads/brat_nova.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND="!sci-biology/brat
+	!sci-biology/brat_bw"
+
+S="${WORKDIR}"/"${PN}"
+
+src_prepare() {
+	sed \
+		-e "s:g++:$(tc-getCXX):g" \
+		-e "s:-O3 -w:${CFLAGS} ${LDFLAGS}:g" \
+		-i Makefile || die
+}
+
+src_install() {
+	dobin brat_bw build_bw trim acgt-count remove-dupl
+	# possible FILE_COLLISION
+	# on these with with sci-biology/brat
+		# trim acgt-count remove-dupl
+	# on these with sci-biology/brat_bw
+		# brat_bw build_bw trim acgt-count remove-dupl
+}

diff --git a/sci-biology/brat_nova/metadata.xml b/sci-biology/brat_nova/metadata.xml
new file mode 100644
index 0000000..004c995
--- /dev/null
+++ b/sci-biology/brat_nova/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_nova/

[Martin Mokrejs]

commit:     d23aff7f42eb30ef45b62968a3c4f4de089aca64
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Sep  1 18:37:20 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Sep  1 18:37:20 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d23aff7f

sci-biology/brat_nova: clarify DESCRIPTION per upstream email

Package-Manager: portage-2.3.0

 sci-biology/brat_nova/brat_nova-20160103.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/brat_nova/brat_nova-20160103.ebuild b/sci-biology/brat_nova/brat_nova-20160103.ebuild
index 3a3fa2b..b4c1bb7 100644
--- a/sci-biology/brat_nova/brat_nova-20160103.ebuild
+++ b/sci-biology/brat_nova/brat_nova-20160103.ebuild
@@ -6,7 +6,7 @@ EAPI=5
 
 inherit toolchain-funcs
 
-DESCRIPTION="Bisulfite-aware short read mapper, FM-index, no InDel support (improved brat_bw)"
+DESCRIPTION="Bisulfite-aware short read mapper, FM-index, accepts 1 InDel/read, local align"
 HOMEPAGE="http://compbio.cs.ucr.edu/brat/"
 SRC_URI="http://compbio.cs.ucr.edu/brat/downloads/brat_nova.tar.gz -> ${P}.tar.gz"
 

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

[Andrew Ammerlaan]

commit:     7bcbd074a1a842df536c3da1fa5cd4bc3c4a146a
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar  6 10:07:12 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar  6 10:07:12 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7bcbd074

sci-biology/brat_nova: EAPI bump

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

 sci-biology/brat_nova/brat_nova-20160103.ebuild | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/sci-biology/brat_nova/brat_nova-20160103.ebuild b/sci-biology/brat_nova/brat_nova-20160103.ebuild
index d67acaeb6..6acb579a6 100644
--- a/sci-biology/brat_nova/brat_nova-20160103.ebuild
+++ b/sci-biology/brat_nova/brat_nova-20160103.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
 
@@ -11,7 +11,6 @@ SRC_URI="http://compbio.cs.ucr.edu/brat/downloads/brat_nova.tar.gz -> ${P}.tar.g
 
 LICENSE="GPL-3"
 SLOT="0"
-IUSE=""
 KEYWORDS="~amd64 ~x86"
 
 DEPEND=""
@@ -21,6 +20,7 @@ RDEPEND="!sci-biology/brat
 S="${WORKDIR}"/"${PN}"
 
 src_prepare() {
+	default
 	sed \
 		-e "s:g++:$(tc-getCXX):g" \
 		-e "s:-O3 -w:${CFLAGS} ${LDFLAGS}:g" \