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

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

[Justin Lecher]

commit:     ebe221d2a8b9dc8ff4a97c56cb376c4249e3d945
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Jun 24 17:20:48 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jun 24 17:20:48 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ebe221d2

SOme ebuild cleaning

(Portage version: 2.2.0_alpha41/git/Linux x86_64, signed Manifest commit with key 70EB7916)

---
 sci-biology/bedtools/ChangeLog              |    7 +++++++
 sci-biology/bedtools/bedtools-2.10.1.ebuild |   18 +++++-------------
 2 files changed, 12 insertions(+), 13 deletions(-)

diff --git a/sci-biology/bedtools/ChangeLog b/sci-biology/bedtools/ChangeLog
new file mode 100644
index 0000000..3fd8071
--- /dev/null
+++ b/sci-biology/bedtools/ChangeLog
@@ -0,0 +1,7 @@
+# ChangeLog for sci-biology/bedtools
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  24 Jun 2011; Justin Lecher <jlec@gentoo.org> bedtools-2.10.1.ebuild:
+  SOme ebuild cleaning
+

diff --git a/sci-biology/bedtools/bedtools-2.10.1.ebuild b/sci-biology/bedtools/bedtools-2.10.1.ebuild
index f03a4f7..541b056 100644
--- a/sci-biology/bedtools/bedtools-2.10.1.ebuild
+++ b/sci-biology/bedtools/bedtools-2.10.1.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=3
+EAPI=4
 
-DESCRIPTION="BEDTools for manipulation and analysis of BED, GFF/GTF, VCF, and SAM/BAM file formats"
+DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, and SAM/BAM file formats"
 HOMEPAGE="http://code.google.com/p/bedtools/"
 SRC_URI="http://bedtools.googlecode.com/files/BEDTools.v${PV}.tar.gz"
 
@@ -13,16 +13,8 @@ SLOT="0"
 KEYWORDS="~x86 ~amd64"
 IUSE=""
 
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-src_compile(){
-	cd BEDTools-Version-2.10.1 || die
-	emake all || die
-}
+S="${WORKDIR}"BEDTools-Version-${PV}
 
 src_install(){
-	cd BEDTools-Version-2.10.1 || die
-	mv bin/overlap bin/bt_ovelap # prevent file collision with sci-biology/wgs-assembler
-	dobin bin/*
+	newbin bin/overlap bt_ovelap
 }

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

[Andrey Kislyuk]

commit:     99bcf3ee67aa271addfb384ad35d8488707a9849
Author:     Andrey Kislyuk <weaver <AT> gentoo <DOT> org>
AuthorDate: Sun Oct  9 04:02:48 2011 +0000
Commit:     Andrey Kislyuk <weaver <AT> gentoo <DOT> org>
CommitDate: Sun Oct  9 04:02:48 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=99bcf3ee

In main tree

---
 sci-biology/bedtools/ChangeLog              |    7 -------
 sci-biology/bedtools/bedtools-2.10.1.ebuild |   20 --------------------
 sci-biology/bedtools/metadata.xml           |   10 ----------
 3 files changed, 0 insertions(+), 37 deletions(-)

diff --git a/sci-biology/bedtools/ChangeLog b/sci-biology/bedtools/ChangeLog
deleted file mode 100644
index 3fd8071..0000000
--- a/sci-biology/bedtools/ChangeLog
+++ /dev/null
@@ -1,7 +0,0 @@
-# ChangeLog for sci-biology/bedtools
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-  24 Jun 2011; Justin Lecher <jlec@gentoo.org> bedtools-2.10.1.ebuild:
-  SOme ebuild cleaning
-

diff --git a/sci-biology/bedtools/bedtools-2.10.1.ebuild b/sci-biology/bedtools/bedtools-2.10.1.ebuild
deleted file mode 100644
index 541b056..0000000
--- a/sci-biology/bedtools/bedtools-2.10.1.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=4
-
-DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, and SAM/BAM file formats"
-HOMEPAGE="http://code.google.com/p/bedtools/"
-SRC_URI="http://bedtools.googlecode.com/files/BEDTools.v${PV}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-IUSE=""
-
-S="${WORKDIR}"BEDTools-Version-${PV}
-
-src_install(){
-	newbin bin/overlap bt_ovelap
-}

diff --git a/sci-biology/bedtools/metadata.xml b/sci-biology/bedtools/metadata.xml
deleted file mode 100644
index 7789d7d..0000000
--- a/sci-biology/bedtools/metadata.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<herd>no-herd</herd>
-	<maintainer>
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<longdescription>BEDTools: a flexible suite of utilities for comparing genomic features.</longdescription>
-</pkgmetadata>

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

[Martin Mokrejs]

commit:     43d38bb3cdfe595def6f13cd1748eda9b1933e27
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Apr 15 21:33:35 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Apr 15 21:33:35 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=43d38bb3

sci-biology/bedtools: version bump per bug #505538

Package-Manager: portage-2.2.7

---
 sci-biology/bedtools/ChangeLog              |  9 ++++++++
 sci-biology/bedtools/bedtools-2.19.1.ebuild | 33 +++++++++++++++++++++++++++++
 sci-biology/bedtools/metadata.xml           | 16 ++++++++++++++
 3 files changed, 58 insertions(+)

diff --git a/sci-biology/bedtools/ChangeLog b/sci-biology/bedtools/ChangeLog
new file mode 100644
index 0000000..530ceb5
--- /dev/null
+++ b/sci-biology/bedtools/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/bedtools
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*bedtools-2.19.1 (15 Apr 2014)
+
+  15 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +bedtools-2.19.1.ebuild, +metadata.xml:
+  sci-biology/bedtools: version bump per bug #505538

diff --git a/sci-biology/bedtools/bedtools-2.19.1.ebuild b/sci-biology/bedtools/bedtools-2.19.1.ebuild
new file mode 100644
index 0000000..fd87585
--- /dev/null
+++ b/sci-biology/bedtools/bedtools-2.19.1.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bedtools/bedtools-2.16.2.ebuild,v 1.1 2012/05/29 02:54:40 weaver Exp $
+
+EAPI=4
+
+inherit flag-o-matic
+
+DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, and SAM/BAM file formats"
+HOMEPAGE="http://code.google.com/p/bedtools/"
+SRC_URI="https://github.com/arq5x/bedtools2/releases/download/v${PV}/bedtools-${PV}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE=""
+
+S="${WORKDIR}/bedtools2-${PV}"
+
+src_prepare() {
+	filter-ldflags -Wl,--as-needed
+	sed -i \
+		-e '/export CXXFLAGS/ d' \
+		-e '/export CXX/ d' \
+		Makefile || die
+}
+
+src_install() {
+	dobin bin/*
+	dodoc README* RELEASE_HISTORY
+	insinto /usr/share/${PN}
+	doins -r genomes
+}

diff --git a/sci-biology/bedtools/metadata.xml b/sci-biology/bedtools/metadata.xml
new file mode 100644
index 0000000..d841c4b
--- /dev/null
+++ b/sci-biology/bedtools/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <herd>proxy-maintainers</herd>
+  <maintainer>
+    <email>mmokrejs@gmail.com</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+  <longdescription>
+    BEDTools: a flexible suite of utilities for comparing genomic features.
+  </longdescription>
+  <upstream>
+    <remote-id type="google-code">bedtools</remote-id>
+  </upstream>
+</pkgmetadata>

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

[Martin Mokrejs]

commit:     8d8a10ea959ea047088b30f52b9004a778db3fa8
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri May 30 13:37:36 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri May 30 13:37:36 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8d8a10ea

sci-biology/bedtools-2.20.1: version bump

Package-Manager: portage-2.2.7

---
 sci-biology/bedtools/ChangeLog                                      | 6 ++++++
 .../bedtools/{bedtools-2.19.1.ebuild => bedtools-2.20.1.ebuild}     | 0
 2 files changed, 6 insertions(+)

diff --git a/sci-biology/bedtools/ChangeLog b/sci-biology/bedtools/ChangeLog
index 530ceb5..031b4f9 100644
--- a/sci-biology/bedtools/ChangeLog
+++ b/sci-biology/bedtools/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*bedtools-2.20.1 (30 May 2014)
+
+  30 May 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +bedtools-2.20.1.ebuild, -bedtools-2.19.1.ebuild:
+  sci-biology/bedtools-2.20.1: version bump
+
 *bedtools-2.19.1 (15 Apr 2014)
 
   15 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>

diff --git a/sci-biology/bedtools/bedtools-2.19.1.ebuild b/sci-biology/bedtools/bedtools-2.20.1.ebuild
similarity index 100%
rename from sci-biology/bedtools/bedtools-2.19.1.ebuild
rename to sci-biology/bedtools/bedtools-2.20.1.ebuild

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

[Martin Mokrejs]

commit:     822634582c5aa77368c8bf6d6b6730d0ee1dd208
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jan 14 23:36:43 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jan 14 23:36:43 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=82263458

drop old version which already landed in main tree; add ebuild for new version

Package-Manager: portage-2.2.7

---
 sci-biology/bedtools/ChangeLog                                    | 8 +++++++-
 .../bedtools/{bedtools-2.20.1.ebuild => bedtools-2.22.1.ebuild}   | 4 ++--
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/sci-biology/bedtools/ChangeLog b/sci-biology/bedtools/ChangeLog
index 031b4f9..a36ef57 100644
--- a/sci-biology/bedtools/ChangeLog
+++ b/sci-biology/bedtools/ChangeLog
@@ -1,7 +1,13 @@
 # ChangeLog for sci-biology/bedtools
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*bedtools-2.22.1 (14 Jan 2015)
+
+  14 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +bedtools-2.22.1.ebuild, -bedtools-2.20.1.ebuild:
+  drop old version which already landed in main tree; add ebuild for new version
+
 *bedtools-2.20.1 (30 May 2014)
 
   30 May 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>

diff --git a/sci-biology/bedtools/bedtools-2.20.1.ebuild b/sci-biology/bedtools/bedtools-2.22.1.ebuild
similarity index 91%
rename from sci-biology/bedtools/bedtools-2.20.1.ebuild
rename to sci-biology/bedtools/bedtools-2.22.1.ebuild
index fd87585..877dcad 100644
--- a/sci-biology/bedtools/bedtools-2.20.1.ebuild
+++ b/sci-biology/bedtools/bedtools-2.22.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-biology/bedtools/bedtools-2.16.2.ebuild,v 1.1 2012/05/29 02:54:40 weaver Exp $
 
@@ -15,7 +15,7 @@ SLOT="0"
 KEYWORDS="~x86 ~amd64"
 IUSE=""
 
-S="${WORKDIR}/bedtools2-${PV}"
+S="${WORKDIR}/bedtools2"
 
 src_prepare() {
 	filter-ldflags -Wl,--as-needed

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

[Justin Lecher]

commit:     34424314c005186109b01c0571f8ff00e8b149cf
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jun  6 10:10:53 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jun  6 10:10:53 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=34424314

sci-biology/bedtools: Bump to EAPI=5

Package-Manager: portage-2.2.20

 sci-biology/bedtools/ChangeLog              | 3 +++
 sci-biology/bedtools/bedtools-2.22.1.ebuild | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/sci-biology/bedtools/ChangeLog b/sci-biology/bedtools/ChangeLog
index 4bb8198..e72833e 100644
--- a/sci-biology/bedtools/ChangeLog
+++ b/sci-biology/bedtools/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  06 Jun 2015; Justin Lecher <jlec@gentoo.org> bedtools-2.22.1.ebuild:
+  sci-biology/bedtools: Bump to EAPI=5
+
   06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml:
   sci-biology/bedtools: Add github to remote-id in metadata.xml
 

diff --git a/sci-biology/bedtools/bedtools-2.22.1.ebuild b/sci-biology/bedtools/bedtools-2.22.1.ebuild
index df72ec7..97a20b3 100644
--- a/sci-biology/bedtools/bedtools-2.22.1.ebuild
+++ b/sci-biology/bedtools/bedtools-2.22.1.ebuild
@@ -2,7 +2,7 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=4
+EAPI=5
 
 inherit flag-o-matic
 

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

[Martin Mokrejs]

commit:     459c9ffc65063046c8954391cc3904bfdffdf084
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Sep 20 15:28:04 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Sep 20 15:28:04 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=459c9ffc

sci-biology/bedtools: version bump

Package-Manager: portage-2.3.0

 sci-biology/bedtools/{bedtools-2.22.1.ebuild => bedtools-2.26.0.ebuild} | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/bedtools/bedtools-2.22.1.ebuild b/sci-biology/bedtools/bedtools-2.26.0.ebuild
similarity index 94%
rename from sci-biology/bedtools/bedtools-2.22.1.ebuild
rename to sci-biology/bedtools/bedtools-2.26.0.ebuild
index 2d79bce..277a3bd 100644
--- a/sci-biology/bedtools/bedtools-2.22.1.ebuild
+++ b/sci-biology/bedtools/bedtools-2.26.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 

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

[Martin Mokrejs]

commit:     16a4e6fa7ee91167da5980f5c0a7bc95214d3b2b
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Sep 20 15:31:34 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Sep 20 15:31:34 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=16a4e6fa

sci-biology/bedtools: shorten DESCRIPTION line

Package-Manager: portage-2.3.0

 sci-biology/bedtools/bedtools-2.26.0.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/bedtools/bedtools-2.26.0.ebuild b/sci-biology/bedtools/bedtools-2.26.0.ebuild
index 277a3bd..4dac032 100644
--- a/sci-biology/bedtools/bedtools-2.26.0.ebuild
+++ b/sci-biology/bedtools/bedtools-2.26.0.ebuild
@@ -6,7 +6,7 @@ EAPI=5
 
 inherit flag-o-matic
 
-DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, and SAM/BAM file formats"
+DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats"
 HOMEPAGE="http://code.google.com/p/bedtools/"
 SRC_URI="https://github.com/arq5x/bedtools2/releases/download/v${PV}/bedtools-${PV}.tar.gz"
 

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

[Martin Mokrejs]

commit:     68340c15e4d4c0275529797f87583b9d141cb227
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Sep 24 09:13:08 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Sep 24 09:13:08 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=68340c15

sci-biology/bedtools: update HOMEPAGE

Package-Manager: portage-2.3.0

 sci-biology/bedtools/bedtools-2.26.0.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/bedtools/bedtools-2.26.0.ebuild b/sci-biology/bedtools/bedtools-2.26.0.ebuild
index 4dac032..d796a3e 100644
--- a/sci-biology/bedtools/bedtools-2.26.0.ebuild
+++ b/sci-biology/bedtools/bedtools-2.26.0.ebuild
@@ -7,7 +7,7 @@ EAPI=5
 inherit flag-o-matic
 
 DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats"
-HOMEPAGE="http://code.google.com/p/bedtools/"
+HOMEPAGE="https://github.com/arq5x/bedtools2"
 SRC_URI="https://github.com/arq5x/bedtools2/releases/download/v${PV}/bedtools-${PV}.tar.gz"
 
 LICENSE="GPL-2"

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

[Martin Mokrejs]

commit:     29f09c80275e0e14527e2e45e91f9aaed8f2af2b
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Oct  3 17:47:40 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Oct  3 17:47:40 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=29f09c80

sci-biology/bedtools: rewritten ebuild landed now in main tree (bug #594994)

 sci-biology/bedtools/bedtools-2.26.0.ebuild | 33 -----------------------------
 sci-biology/bedtools/metadata.xml           | 23 --------------------
 2 files changed, 56 deletions(-)

diff --git a/sci-biology/bedtools/bedtools-2.26.0.ebuild b/sci-biology/bedtools/bedtools-2.26.0.ebuild
deleted file mode 100644
index d796a3e..0000000
--- a/sci-biology/bedtools/bedtools-2.26.0.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit flag-o-matic
-
-DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats"
-HOMEPAGE="https://github.com/arq5x/bedtools2"
-SRC_URI="https://github.com/arq5x/bedtools2/releases/download/v${PV}/bedtools-${PV}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-IUSE=""
-
-S="${WORKDIR}/bedtools2"
-
-src_prepare() {
-	filter-ldflags -Wl,--as-needed
-	sed -i \
-		-e '/export CXXFLAGS/ d' \
-		-e '/export CXX/ d' \
-		Makefile || die
-}
-
-src_install() {
-	dobin bin/*
-	dodoc README* RELEASE_HISTORY
-	insinto /usr/share/${PN}
-	doins -r genomes
-}

diff --git a/sci-biology/bedtools/metadata.xml b/sci-biology/bedtools/metadata.xml
deleted file mode 100644
index 39869a9..0000000
--- a/sci-biology/bedtools/metadata.xml
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="person">
-    <email>mmokrejs@gmail.com</email>
-    <name>Martin Mokrejs</name>
-  </maintainer>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <maintainer type="project">
-    <email>proxy-maint@gentoo.org</email>
-    <name>Proxy Maintainers</name>
-  </maintainer>
-  <longdescription>
-    BEDTools: a flexible suite of utilities for comparing genomic features.
-  </longdescription>
-  <upstream>
-    <remote-id type="google-code">bedtools</remote-id>
-    <remote-id type="github">arq5x/bedtools2</remote-id>
-  </upstream>
-</pkgmetadata>

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

[Marius Brehler]

commit:     cc5e3c7ccf16087d32e5c933f2f9e0307ce1900f
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Sep 24 23:00:27 2016 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Sat Sep 24 23:02:50 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=cc5e3c7c

sci-biology/bedtools: remove, in main tree

 sci-biology/bedtools/bedtools-2.26.0.ebuild | 33 -----------------------------
 sci-biology/bedtools/metadata.xml           | 23 --------------------
 2 files changed, 56 deletions(-)

diff --git a/sci-biology/bedtools/bedtools-2.26.0.ebuild b/sci-biology/bedtools/bedtools-2.26.0.ebuild
deleted file mode 100644
index 4dac032..0000000
--- a/sci-biology/bedtools/bedtools-2.26.0.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit flag-o-matic
-
-DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats"
-HOMEPAGE="http://code.google.com/p/bedtools/"
-SRC_URI="https://github.com/arq5x/bedtools2/releases/download/v${PV}/bedtools-${PV}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-IUSE=""
-
-S="${WORKDIR}/bedtools2"
-
-src_prepare() {
-	filter-ldflags -Wl,--as-needed
-	sed -i \
-		-e '/export CXXFLAGS/ d' \
-		-e '/export CXX/ d' \
-		Makefile || die
-}
-
-src_install() {
-	dobin bin/*
-	dodoc README* RELEASE_HISTORY
-	insinto /usr/share/${PN}
-	doins -r genomes
-}

diff --git a/sci-biology/bedtools/metadata.xml b/sci-biology/bedtools/metadata.xml
deleted file mode 100644
index 39869a9..0000000
--- a/sci-biology/bedtools/metadata.xml
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="person">
-    <email>mmokrejs@gmail.com</email>
-    <name>Martin Mokrejs</name>
-  </maintainer>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <maintainer type="project">
-    <email>proxy-maint@gentoo.org</email>
-    <name>Proxy Maintainers</name>
-  </maintainer>
-  <longdescription>
-    BEDTools: a flexible suite of utilities for comparing genomic features.
-  </longdescription>
-  <upstream>
-    <remote-id type="google-code">bedtools</remote-id>
-    <remote-id type="github">arq5x/bedtools2</remote-id>
-  </upstream>
-</pkgmetadata>