* [gentoo-commits] proj/sci:master commit in: sci-biology/Atlas_GapFill/
@ 2015-01-07 22:25 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2015-01-07 22:25 UTC (permalink / raw
To: gentoo-commits
commit: 86160d6d6d042a10bd3b1a8b432eaf6db560b6d3
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jan 7 22:24:19 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jan 7 22:24:19 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=86160d6d
Initial ebuild
---
sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild | 23 ++++++++++++++++++++++
sci-biology/Atlas_GapFill/ChangeLog | 10 ++++++++++
sci-biology/Atlas_GapFill/metadata.xml | 9 +++++++++
3 files changed, 42 insertions(+)
diff --git a/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild b/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild
new file mode 100644
index 0000000..c658019
--- /dev/null
+++ b/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Close gaps using BWA-identified reads and reassemble using Phrap, Newbler, Velvet, compare by cross_match"
+HOMEPAGE="https://www.hgsc.bcm.edu/software/atlas-gapfill"
+SRC_URI="https://www.hgsc.bcm.edu/sites/default/files/software/ATLAS_GapFill_V2_2/ATLAS_GapFill_V2.2_release.tar.bz2
+ https://www.hgsc.bcm.edu/sites/default/files/software/ATLAS_GapFill_V2_2/README -> ATLAS_GapFill_V2_2.README"
+
+LICENSE=""
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+# is there an ebuild for newbler so we could add it to DEPEND?
+DEPEND="dev-lang/perl
+ sys-cluster/torque || ( sys-cluster/openpbs )
+ sci-biology/phrap
+ sci-biology/bwa
+ sci-biology/velvet"
+RDEPEND="${DEPEND}"
diff --git a/sci-biology/Atlas_GapFill/ChangeLog b/sci-biology/Atlas_GapFill/ChangeLog
new file mode 100644
index 0000000..74cc2d8
--- /dev/null
+++ b/sci-biology/Atlas_GapFill/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/Atlas_GapFill
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*Atlas_GapFill-2.2 (07 Jan 2015)
+
+ 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +Atlas_GapFill-2.2.ebuild, +metadata.xml:
+ initial ebuild
+
diff --git a/sci-biology/Atlas_GapFill/metadata.xml b/sci-biology/Atlas_GapFill/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/Atlas_GapFill/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] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/Atlas_GapFill/
@ 2015-01-10 14:07 Justin Lecher
0 siblings, 0 replies; 5+ messages in thread
From: Justin Lecher @ 2015-01-10 14:07 UTC (permalink / raw
To: gentoo-commits
commit: 758306af1aa25823c98b475b05c1dfa672a2c3fc
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 10 13:50:11 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan 10 13:50:11 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=758306af
sci-biology/Atlas_GapFill: Fix license
Package-Manager: portage-2.2.15
---
sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild | 15 ++++++++++-----
sci-biology/Atlas_GapFill/ChangeLog | 3 +++
2 files changed, 13 insertions(+), 5 deletions(-)
diff --git a/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild b/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild
index c658019..2985d23 100644
--- a/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild
+++ b/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild
@@ -4,19 +4,24 @@
EAPI=5
-DESCRIPTION="Close gaps using BWA-identified reads and reassemble using Phrap, Newbler, Velvet, compare by cross_match"
+DESCRIPTION="Close gaps using BWA-identified reads and reassemble"
HOMEPAGE="https://www.hgsc.bcm.edu/software/atlas-gapfill"
-SRC_URI="https://www.hgsc.bcm.edu/sites/default/files/software/ATLAS_GapFill_V2_2/ATLAS_GapFill_V2.2_release.tar.bz2
+SRC_URI="
+ https://www.hgsc.bcm.edu/sites/default/files/software/ATLAS_GapFill_V2_2/ATLAS_GapFill_V2.2_release.tar.bz2
https://www.hgsc.bcm.edu/sites/default/files/software/ATLAS_GapFill_V2_2/README -> ATLAS_GapFill_V2_2.README"
-LICENSE=""
+LICENSE="ATLAS"
SLOT="0"
KEYWORDS=""
IUSE=""
# is there an ebuild for newbler so we could add it to DEPEND?
-DEPEND="dev-lang/perl
- sys-cluster/torque || ( sys-cluster/openpbs )
+DEPEND="
+ dev-lang/perl
+ || (
+ sys-cluster/openpbs
+ sys-cluster/torque
+ )
sci-biology/phrap
sci-biology/bwa
sci-biology/velvet"
diff --git a/sci-biology/Atlas_GapFill/ChangeLog b/sci-biology/Atlas_GapFill/ChangeLog
index 74cc2d8..7504c07 100644
--- a/sci-biology/Atlas_GapFill/ChangeLog
+++ b/sci-biology/Atlas_GapFill/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 10 Jan 2015; Justin Lecher <jlec@gentoo.org> Atlas_GapFill-2.2.ebuild:
+ Fix license
+
*Atlas_GapFill-2.2 (07 Jan 2015)
07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/Atlas_GapFill/
@ 2015-02-18 16:41 Justin Lecher
0 siblings, 0 replies; 5+ messages in thread
From: Justin Lecher @ 2015-02-18 16:41 UTC (permalink / raw
To: gentoo-commits
commit: 95fd222a338248d5a322670bc14b9e470514134e
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 18 13:40:58 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 18 13:40:58 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=95fd222a
sci-biology/Atlas_GapFill: drop unknown dep
Package-Manager: portage-2.2.17
---
sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild | 9 +++------
sci-biology/Atlas_GapFill/ChangeLog | 4 +++-
2 files changed, 6 insertions(+), 7 deletions(-)
diff --git a/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild b/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild
index 2985d23..2206036 100644
--- a/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild
+++ b/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild
@@ -16,13 +16,10 @@ KEYWORDS=""
IUSE=""
# is there an ebuild for newbler so we could add it to DEPEND?
-DEPEND="
+RDEPEND="
dev-lang/perl
- || (
- sys-cluster/openpbs
- sys-cluster/torque
- )
+ sys-cluster/torque
sci-biology/phrap
sci-biology/bwa
sci-biology/velvet"
-RDEPEND="${DEPEND}"
+DEPEND=""
diff --git a/sci-biology/Atlas_GapFill/ChangeLog b/sci-biology/Atlas_GapFill/ChangeLog
index 7504c07..abaf634 100644
--- a/sci-biology/Atlas_GapFill/ChangeLog
+++ b/sci-biology/Atlas_GapFill/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 18 Feb 2015; Justin Lecher <jlec@gentoo.org> Atlas_GapFill-2.2.ebuild:
+ sci-biology/Atlas_GapFill: drop unknown dep
+
10 Jan 2015; Justin Lecher <jlec@gentoo.org> Atlas_GapFill-2.2.ebuild:
Fix license
@@ -10,4 +13,3 @@
07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+Atlas_GapFill-2.2.ebuild, +metadata.xml:
initial ebuild
-
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/Atlas_GapFill/
@ 2017-02-21 11:48 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2017-02-21 11:48 UTC (permalink / raw
To: gentoo-commits
commit: 89126c586173488f6c1356163f18aca8b4d191c9
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Feb 21 11:48:29 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Feb 21 11:48:29 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=89126c58
sci-biology/Atlas_GapFill: remove dependency on sys-cluster/torque
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild b/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild
index e3681243f..a8643695e 100644
--- a/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild
+++ b/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -18,7 +18,6 @@ IUSE=""
# is there an ebuild for newbler so we could add it to DEPEND?
RDEPEND="
dev-lang/perl
- sys-cluster/torque
sci-biology/phrap
sci-biology/bwa
sci-biology/velvet"
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/Atlas_GapFill/
@ 2020-09-27 22:43 Horea Christian
0 siblings, 0 replies; 5+ messages in thread
From: Horea Christian @ 2020-09-27 22:43 UTC (permalink / raw
To: gentoo-commits
commit: 445e6bd8a1fbcd0c93bd0509a467b6bb75a1d265
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun Sep 27 22:37:20 2020 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Sep 27 22:43:20 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=445e6bd8
sci-biology/Atlas_GapFill: removed discontinued package
Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild | 23 ----------------------
sci-biology/Atlas_GapFill/metadata.xml | 12 -----------
2 files changed, 35 deletions(-)
diff --git a/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild b/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild
deleted file mode 100644
index 935134f09..000000000
--- a/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Close gaps using BWA-identified reads and reassemble"
-HOMEPAGE="https://www.hgsc.bcm.edu/software/atlas-gapfill"
-SRC_URI="
- https://www.hgsc.bcm.edu/sites/default/files/software/ATLAS_GapFill_V2_2/ATLAS_GapFill_V2.2_release.tar.bz2
- https://www.hgsc.bcm.edu/sites/default/files/software/ATLAS_GapFill_V2_2/README -> ATLAS_GapFill_V2_2.README"
-
-LICENSE="ATLAS"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-# is there an ebuild for newbler so we could add it to DEPEND?
-RDEPEND="
- dev-lang/perl
- sci-biology/phrap
- sci-biology/bwa
- sci-biology/velvet"
-DEPEND=""
diff --git a/sci-biology/Atlas_GapFill/metadata.xml b/sci-biology/Atlas_GapFill/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/Atlas_GapFill/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] 5+ messages in thread
end of thread, other threads:[~2020-09-27 22:43 UTC | newest]
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