* [gentoo-commits] proj/sci:master commit in: sci-biology/breakdancer/
@ 2014-03-23 17:11 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2014-03-23 17:11 UTC (permalink / raw
To: gentoo-commits
commit: b48f9a93a42d45079330c7b9ecfc27ba5570ac1b
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 17:10:18 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 17:10:18 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b48f9a93
sci-biology/breakdancer: a skeleton for a new package, needs perl help
Package-Manager: portage-2.2.7
---
sci-biology/breakdancer/ChangeLog | 9 +++++++++
sci-biology/breakdancer/breakdancer-1.1.2.ebuild | 20 ++++++++++++++++++++
sci-biology/breakdancer/metadata.xml | 9 +++++++++
3 files changed, 38 insertions(+)
diff --git a/sci-biology/breakdancer/ChangeLog b/sci-biology/breakdancer/ChangeLog
new file mode 100644
index 0000000..2dfc569
--- /dev/null
+++ b/sci-biology/breakdancer/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/breakdancer
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*breakdancer-1.1.2 (23 Mar 2014)
+
+ 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +breakdancer-1.1.2.ebuild, +metadata.xml:
+ sci-biology/breakdancer: a skeleton for a new package, needs perl help
diff --git a/sci-biology/breakdancer/breakdancer-1.1.2.ebuild b/sci-biology/breakdancer/breakdancer-1.1.2.ebuild
new file mode 100644
index 0000000..6aff868
--- /dev/null
+++ b/sci-biology/breakdancer/breakdancer-1.1.2.ebuild
@@ -0,0 +1,20 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Genome-wide detection of structural variants from next generation paired-end sequencing reads"
+HOMEPAGE="http://breakdancer.sourceforge.net"
+SRC_URI="http://sourceforge.net/projects/breakdancer/files/breakdancer-1.1.2_2013_03_08.zip"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="dev-lang/perl
+ dev-perl/Statistics-Descriptive
+ dev-perl/Math-CDF
+ sci-biology/samtools"
+RDEPEND="${DEPEND}"
diff --git a/sci-biology/breakdancer/metadata.xml b/sci-biology/breakdancer/metadata.xml
new file mode 100644
index 0000000..07b5255
--- /dev/null
+++ b/sci-biology/breakdancer/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/breakdancer/
@ 2015-05-18 22:01 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2015-05-18 22:01 UTC (permalink / raw
To: gentoo-commits
commit: a064c41bd0283321afe151af6a49e83873bade3f
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon May 18 22:01:27 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon May 18 22:01:27 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a064c41b
sci-biology/breakdancer: upstream moved to github
Package-Manager: portage-2.2.18
sci-biology/breakdancer/ChangeLog | 8 ++++-
sci-biology/breakdancer/breakdancer-1.1.2.ebuild | 20 ------------
sci-biology/breakdancer/breakdancer-9999.ebuild | 40 ++++++++++++++++++++++++
3 files changed, 47 insertions(+), 21 deletions(-)
diff --git a/sci-biology/breakdancer/ChangeLog b/sci-biology/breakdancer/ChangeLog
index 2dfc569..1fbaee5 100644
--- a/sci-biology/breakdancer/ChangeLog
+++ b/sci-biology/breakdancer/ChangeLog
@@ -1,7 +1,13 @@
# ChangeLog for sci-biology/breakdancer
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*breakdancer-9999 (18 May 2015)
+
+ 18 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +breakdancer-9999.ebuild, -Manifest, -breakdancer-1.1.2.ebuild:
+ sci-biology/breakdancer: upstream moved to github
+
*breakdancer-1.1.2 (23 Mar 2014)
23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/breakdancer/breakdancer-1.1.2.ebuild b/sci-biology/breakdancer/breakdancer-1.1.2.ebuild
deleted file mode 100644
index 6aff868..0000000
--- a/sci-biology/breakdancer/breakdancer-1.1.2.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-DESCRIPTION="Genome-wide detection of structural variants from next generation paired-end sequencing reads"
-HOMEPAGE="http://breakdancer.sourceforge.net"
-SRC_URI="http://sourceforge.net/projects/breakdancer/files/breakdancer-1.1.2_2013_03_08.zip"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="dev-lang/perl
- dev-perl/Statistics-Descriptive
- dev-perl/Math-CDF
- sci-biology/samtools"
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/breakdancer/breakdancer-9999.ebuild b/sci-biology/breakdancer/breakdancer-9999.ebuild
new file mode 100644
index 0000000..11888b4
--- /dev/null
+++ b/sci-biology/breakdancer/breakdancer-9999.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+[ "$PV" == "9999" ] && inherit git-r3
+
+PERL_EXPORT_PHASE_FUNCTIONS=no
+inherit perl-module eutils toolchain-funcs
+
+DESCRIPTION="Genome-wide detection of structural variants from next generation paired-end sequencing reads"
+HOMEPAGE="http://breakdancer.sourceforge.net"
+if [ "$PV" == "9999" ]; then
+ EGIT_REPO_URI="https://github.com/genome/breakdancer.git"
+ KEYWORDS=""
+else
+ # TODO: fish out 1.3.6 version from github
+ SRC_URI="http://sourceforge.net/projects/breakdancer/files/breakdancer-1.1.2_2013_03_08.zip"
+ KEYWORDS=""
+fi
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+
+# http://search.cpan.org/~callahan/Math-CDF-0.1/CDF.pm
+DEPEND="dev-lang/perl
+ dev-perl/Statistics-Descriptive
+ sci-biology/samtools"
+RDEPEND="${DEPEND}"
+
+# cd breakdancer
+# mkdir build
+# cd build
+# cmake .. -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local
+# ...
+# -- Build files have been written to: .../breakdancer/build
+# make
+# make install
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/breakdancer/
@ 2015-05-18 22:04 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2015-05-18 22:04 UTC (permalink / raw
To: gentoo-commits
commit: 842701de2c0be821e45401806d93123d21dc8865
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon May 18 22:04:31 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon May 18 22:04:31 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=842701de
sci-biology/breakdancer: update homepage
Package-Manager: portage-2.2.18
sci-biology/breakdancer/ChangeLog | 4 ++++
sci-biology/breakdancer/breakdancer-9999.ebuild | 2 +-
2 files changed, 5 insertions(+), 1 deletion(-)
diff --git a/sci-biology/breakdancer/ChangeLog b/sci-biology/breakdancer/ChangeLog
index 1fbaee5..eba1f9c 100644
--- a/sci-biology/breakdancer/ChangeLog
+++ b/sci-biology/breakdancer/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 18 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ breakdancer-9999.ebuild:
+ sci-biology/breakdancer: update homepage
+
*breakdancer-9999 (18 May 2015)
18 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/breakdancer/breakdancer-9999.ebuild b/sci-biology/breakdancer/breakdancer-9999.ebuild
index 11888b4..21cd2ff 100644
--- a/sci-biology/breakdancer/breakdancer-9999.ebuild
+++ b/sci-biology/breakdancer/breakdancer-9999.ebuild
@@ -10,7 +10,7 @@ PERL_EXPORT_PHASE_FUNCTIONS=no
inherit perl-module eutils toolchain-funcs
DESCRIPTION="Genome-wide detection of structural variants from next generation paired-end sequencing reads"
-HOMEPAGE="http://breakdancer.sourceforge.net"
+HOMEPAGE="http://gmt.genome.wustl.edu/packages/breakdancer"
if [ "$PV" == "9999" ]; then
EGIT_REPO_URI="https://github.com/genome/breakdancer.git"
KEYWORDS=""
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/breakdancer/
@ 2015-05-18 23:15 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2015-05-18 23:15 UTC (permalink / raw
To: gentoo-commits
commit: 246dea86fede89662bc24350498bafb6b1634786
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon May 18 23:14:46 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon May 18 23:14:46 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=246dea86
sci-biology/breakdancer: added inherit cmake
Package-Manager: portage-2.2.18
sci-biology/breakdancer/ChangeLog | 4 ++++
sci-biology/breakdancer/breakdancer-9999.ebuild | 11 ++---------
2 files changed, 6 insertions(+), 9 deletions(-)
diff --git a/sci-biology/breakdancer/ChangeLog b/sci-biology/breakdancer/ChangeLog
index eba1f9c..d577653 100644
--- a/sci-biology/breakdancer/ChangeLog
+++ b/sci-biology/breakdancer/ChangeLog
@@ -4,6 +4,10 @@
18 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
breakdancer-9999.ebuild:
+ sci-biology/breakdancer: added inherit cmake
+
+ 18 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ breakdancer-9999.ebuild:
sci-biology/breakdancer: update homepage
*breakdancer-9999 (18 May 2015)
diff --git a/sci-biology/breakdancer/breakdancer-9999.ebuild b/sci-biology/breakdancer/breakdancer-9999.ebuild
index 21cd2ff..c0599b3 100644
--- a/sci-biology/breakdancer/breakdancer-9999.ebuild
+++ b/sci-biology/breakdancer/breakdancer-9999.ebuild
@@ -4,6 +4,8 @@
EAPI=5
+inherit cmake-utils
+
[ "$PV" == "9999" ] && inherit git-r3
PERL_EXPORT_PHASE_FUNCTIONS=no
@@ -29,12 +31,3 @@ DEPEND="dev-lang/perl
dev-perl/Statistics-Descriptive
sci-biology/samtools"
RDEPEND="${DEPEND}"
-
-# cd breakdancer
-# mkdir build
-# cd build
-# cmake .. -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local
-# ...
-# -- Build files have been written to: .../breakdancer/build
-# make
-# make install
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/breakdancer/
@ 2017-01-29 14:20 Justin Lecher
0 siblings, 0 replies; 6+ messages in thread
From: Justin Lecher @ 2017-01-29 14:20 UTC (permalink / raw
To: gentoo-commits
commit: c18962d9d1d8cb9c13caafaaaa7b8204c2b4a885
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 29 14:03:22 2017 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jan 29 14:03:22 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c18962d9
sci-biology/breakdancer: QA fixes
Bump to6 EAPI
drop non active code
add missing slot operator
Convert to perl-functions.eclass
Shorten DESCRIPTION
Package-Manager: Portage-2.3.3, Repoman-2.3.1
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/breakdancer/breakdancer-9999.ebuild | 28 ++++++++-----------------
sci-biology/breakdancer/metadata.xml | 2 +-
2 files changed, 10 insertions(+), 20 deletions(-)
diff --git a/sci-biology/breakdancer/breakdancer-9999.ebuild b/sci-biology/breakdancer/breakdancer-9999.ebuild
index 10d2adb..32688e5 100644
--- a/sci-biology/breakdancer/breakdancer-9999.ebuild
+++ b/sci-biology/breakdancer/breakdancer-9999.ebuild
@@ -1,33 +1,23 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
-EAPI=5
+EAPI=6
-inherit cmake-utils
+inherit cmake-utils git-r3 perl-functions
-[ "$PV" == "9999" ] && inherit git-r3
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs
-
-DESCRIPTION="Genome-wide detection of structural variants from next generation paired-end sequencing reads"
+DESCRIPTION="Genome-wide detection of structural variants from paired-end sequencing reads"
HOMEPAGE="http://gmt.genome.wustl.edu/packages/breakdancer"
-if [ "$PV" == "9999" ]; then
- EGIT_REPO_URI="https://github.com/genome/breakdancer.git"
- KEYWORDS=""
-else
- # TODO: fish out 1.3.6 version from github
- SRC_URI="http://sourceforge.net/projects/breakdancer/files/breakdancer-1.1.2_2013_03_08.zip"
- KEYWORDS=""
-fi
+EGIT_REPO_URI="https://github.com/genome/breakdancer.git"
LICENSE="GPL-3"
SLOT="0"
IUSE=""
+KEYWORDS=""
# http://search.cpan.org/~callahan/Math-CDF-0.1/CDF.pm
-DEPEND="dev-lang/perl
+DEPEND="
+ dev-lang/perl
dev-perl/Statistics-Descriptive
- sci-biology/samtools"
+ sci-biology/samtools:0"
RDEPEND="${DEPEND}"
diff --git a/sci-biology/breakdancer/metadata.xml b/sci-biology/breakdancer/metadata.xml
index 1d67411..138cb77 100644
--- a/sci-biology/breakdancer/metadata.xml
+++ b/sci-biology/breakdancer/metadata.xml
@@ -5,7 +5,7 @@
<email>mmokrejs@fold.natur.cuni.cz</email>
<name>Martin Mokrejs</name>
</maintainer>
-<maintainer type="project">
+ <maintainer type="project">
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/breakdancer/
@ 2021-01-24 14:05 Andrew Ammerlaan
0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2021-01-24 14:05 UTC (permalink / raw
To: gentoo-commits
commit: 2a10d78f128dc80ac3713ffed5adbaa61ca3a6fe
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sun Jan 24 14:05:05 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sun Jan 24 14:05:05 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=2a10d78f
sci-biology/breakdancer: remove pack, repo archived, last update 2015, does not sync
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/breakdancer/breakdancer-9999.ebuild | 22 ----------------------
sci-biology/breakdancer/metadata.xml | 12 ------------
2 files changed, 34 deletions(-)
diff --git a/sci-biology/breakdancer/breakdancer-9999.ebuild b/sci-biology/breakdancer/breakdancer-9999.ebuild
deleted file mode 100644
index 9944acce4..000000000
--- a/sci-biology/breakdancer/breakdancer-9999.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils git-r3 perl-functions
-
-DESCRIPTION="Genome-wide detection of structural variants from paired-end sequencing reads"
-HOMEPAGE="http://gmt.genome.wustl.edu/packages/breakdancer"
-EGIT_REPO_URI="https://github.com/genome/breakdancer.git"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-KEYWORDS=""
-
-# http://search.cpan.org/~callahan/Math-CDF-0.1/CDF.pm
-DEPEND="
- dev-lang/perl
- dev-perl/Statistics-Descriptive
- sci-biology/samtools:0"
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/breakdancer/metadata.xml b/sci-biology/breakdancer/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/breakdancer/metadata.xml
+++ /dev/null
@@ -1,12 +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@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
^ permalink raw reply related [flat|nested] 6+ messages in thread
end of thread, other threads:[~2021-01-24 14:05 UTC | newest]
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