* [gentoo-commits] proj/sci:master commit in: sci-biology/pb-honey/
@ 2015-01-07 21:59 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2015-01-07 21:59 UTC (permalink / raw
To: gentoo-commits
commit: 13ba695f8aa01b1e62f9a6c0a9f99ce940d9aadc
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jan 7 21:58:12 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jan 7 21:58:12 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=13ba695f
initial ebuild for a new package
---
sci-biology/pb-honey/metadata.xml | 9 +++++++++
sci-biology/pb-honey/pb-honey-14.1.15.ebuild | 25 +++++++++++++++++++++++++
2 files changed, 34 insertions(+)
diff --git a/sci-biology/pb-honey/metadata.xml b/sci-biology/pb-honey/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/pb-honey/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>
diff --git a/sci-biology/pb-honey/pb-honey-14.1.15.ebuild b/sci-biology/pb-honey/pb-honey-14.1.15.ebuild
new file mode 100644
index 0000000..c5440bb
--- /dev/null
+++ b/sci-biology/pb-honey/pb-honey-14.1.15.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit distutils-r1
+
+DESCRIPTION="Structural variant identification (SNV) using long reads (over 10kbp)"
+HOMEPAGE="https://www.hgsc.bcm.edu/software/honey"
+SRC_URI="http://sourceforge.net/projects/pb-jelly/files/PBHoney/PBHoney_14.1.15.tgz"
+
+LICENSE=""
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="sci-biology/samtools
+ sci-biology/blasr
+ sci-biology/pysam
+ dev-python/h5py
+ dev-python/numpy"
+RDEPEND="${DEPEND}"
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/pb-honey/
@ 2015-01-10 14:37 Justin Lecher
0 siblings, 0 replies; 5+ messages in thread
From: Justin Lecher @ 2015-01-10 14:37 UTC (permalink / raw
To: gentoo-commits
commit: 5c10a2ccb85f7ccaf754dff2edbdff03f62de1e5
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 10 14:31:05 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan 10 14:31:05 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5c10a2cc
sci-biology/pb-honey: Fix license; add missing []
Package-Manager: portage-2.2.15
---
sci-biology/pb-honey/ChangeLog | 7 +++++++
sci-biology/pb-honey/pb-honey-14.1.15.ebuild | 13 +++++++------
2 files changed, 14 insertions(+), 6 deletions(-)
diff --git a/sci-biology/pb-honey/ChangeLog b/sci-biology/pb-honey/ChangeLog
new file mode 100644
index 0000000..f5e93dc
--- /dev/null
+++ b/sci-biology/pb-honey/ChangeLog
@@ -0,0 +1,7 @@
+# ChangeLog for sci-biology/pb-honey
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 10 Jan 2015; Justin Lecher <jlec@gentoo.org> pb-honey-14.1.15.ebuild:
+ Fix license; add missing []
+
diff --git a/sci-biology/pb-honey/pb-honey-14.1.15.ebuild b/sci-biology/pb-honey/pb-honey-14.1.15.ebuild
index c5440bb..0c3bfef 100644
--- a/sci-biology/pb-honey/pb-honey-14.1.15.ebuild
+++ b/sci-biology/pb-honey/pb-honey-14.1.15.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: $
@@ -12,14 +12,15 @@ DESCRIPTION="Structural variant identification (SNV) using long reads (over 10kb
HOMEPAGE="https://www.hgsc.bcm.edu/software/honey"
SRC_URI="http://sourceforge.net/projects/pb-jelly/files/PBHoney/PBHoney_14.1.15.tgz"
-LICENSE=""
+LICENSE="BSD-2"
SLOT="0"
KEYWORDS=""
IUSE=""
-DEPEND="sci-biology/samtools
+DEPEND="
+ sci-biology/samtools
sci-biology/blasr
- sci-biology/pysam
- dev-python/h5py
- dev-python/numpy"
+ sci-biology/pysam[${PYTHON_USEDEP}]
+ dev-python/h5py[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]"
RDEPEND="${DEPEND}"
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/pb-honey/
@ 2015-05-02 16:29 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2015-05-02 16:29 UTC (permalink / raw
To: gentoo-commits
commit: 52e53a57179d94f4361ce2238b21975a821cf04d
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat May 2 16:11:23 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat May 2 16:11:23 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=52e53a57
added PYTHON_USEDEP
Package-Manager: portage-2.2.18
sci-biology/pb-honey/ChangeLog | 5 ++++-
sci-biology/pb-honey/pb-honey-14.1.15.ebuild | 2 +-
2 files changed, 5 insertions(+), 2 deletions(-)
diff --git a/sci-biology/pb-honey/ChangeLog b/sci-biology/pb-honey/ChangeLog
index f5e93dc..e8c26e9 100644
--- a/sci-biology/pb-honey/ChangeLog
+++ b/sci-biology/pb-honey/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ pb-honey-14.1.15.ebuild:
+ added PYTHON_USEDEP
+
10 Jan 2015; Justin Lecher <jlec@gentoo.org> pb-honey-14.1.15.ebuild:
Fix license; add missing []
-
diff --git a/sci-biology/pb-honey/pb-honey-14.1.15.ebuild b/sci-biology/pb-honey/pb-honey-14.1.15.ebuild
index 0c3bfef..1d91765 100644
--- a/sci-biology/pb-honey/pb-honey-14.1.15.ebuild
+++ b/sci-biology/pb-honey/pb-honey-14.1.15.ebuild
@@ -18,7 +18,7 @@ KEYWORDS=""
IUSE=""
DEPEND="
- sci-biology/samtools
+ sci-biology/samtools[${PYTHON_USEDEP}]
sci-biology/blasr
sci-biology/pysam[${PYTHON_USEDEP}]
dev-python/h5py[${PYTHON_USEDEP}]
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/pb-honey/
@ 2017-01-29 14:20 Justin Lecher
0 siblings, 0 replies; 5+ messages in thread
From: Justin Lecher @ 2017-01-29 14:20 UTC (permalink / raw
To: gentoo-commits
commit: 6764329ca3a139ba9df32f05b74393a1e7d5fa44
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 29 14:20:34 2017 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jan 29 14:20:34 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=6764329c
sci-biology/pb-honey: QA fixes
Bump to EAPI 6
add missing slot operator
Package-Manager: Portage-2.3.3, Repoman-2.3.1
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/pb-honey/pb-honey-14.1.15.ebuild | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/pb-honey/pb-honey-14.1.15.ebuild b/sci-biology/pb-honey/pb-honey-14.1.15.ebuild
index 726840e..ba62451 100644
--- a/sci-biology/pb-honey/pb-honey-14.1.15.ebuild
+++ b/sci-biology/pb-honey/pb-honey-14.1.15.ebuild
@@ -1,8 +1,8 @@
-# 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
PYTHON_COMPAT=( python2_7 )
@@ -18,9 +18,9 @@ KEYWORDS=""
IUSE=""
DEPEND="
- sci-biology/samtools[${PYTHON_USEDEP}]
sci-biology/blasr
sci-biology/pysam[${PYTHON_USEDEP}]
+ sci-biology/samtools:0[${PYTHON_USEDEP}]
dev-python/h5py[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]"
RDEPEND="${DEPEND}"
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/pb-honey/
@ 2020-09-27 20:59 Horea Christian
0 siblings, 0 replies; 5+ messages in thread
From: Horea Christian @ 2020-09-27 20:59 UTC (permalink / raw
To: gentoo-commits
commit: f8c18e63a7bd3240ee469df7638e037c8b3e6b64
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun Sep 27 20:57:50 2020 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Sep 27 20:57:50 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f8c18e63
sci-biology/pb-honey: removed discontinued package
Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/pb-honey/metadata.xml | 15 ---------------
sci-biology/pb-honey/pb-honey-14.1.15.ebuild | 25 -------------------------
2 files changed, 40 deletions(-)
diff --git a/sci-biology/pb-honey/metadata.xml b/sci-biology/pb-honey/metadata.xml
deleted file mode 100644
index 1b533d8a5..000000000
--- a/sci-biology/pb-honey/metadata.xml
+++ /dev/null
@@ -1,15 +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>
- <upstream>
- <remote-id type="sourceforge">pb-jelly</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/pb-honey/pb-honey-14.1.15.ebuild b/sci-biology/pb-honey/pb-honey-14.1.15.ebuild
deleted file mode 100644
index 1a4e10778..000000000
--- a/sci-biology/pb-honey/pb-honey-14.1.15.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Structural variant identification (SNV) using long reads (over 10kbp)"
-HOMEPAGE="https://www.hgsc.bcm.edu/software/honey"
-SRC_URI="http://sourceforge.net/projects/pb-jelly/files/PBHoney/PBHoney_14.1.15.tgz"
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
- sci-biology/blasr
- sci-biology/pysam[${PYTHON_USEDEP}]
- sci-biology/samtools:0[${PYTHON_USEDEP}]
- dev-python/h5py[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]"
-RDEPEND="${DEPEND}"
^ permalink raw reply related [flat|nested] 5+ messages in thread
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