* [gentoo-commits] proj/sci:master commit in: sci-biology/argo-bin/
@ 2011-06-24 17:09 Justin Lecher
0 siblings, 0 replies; 6+ messages in thread
From: Justin Lecher @ 2011-06-24 17:09 UTC (permalink / raw
To: gentoo-commits
commit: 35fe38c58a5036103cbfb3e4181ad8738ca7cd6c
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Jun 24 12:46:53 2011 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jun 24 12:46:53 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=35fe38c5
Sort inherit and/or USE
(Portage version: 2.2.0_alpha41/git/Linux x86_64, signed Manifest commit with key 70EB7916)
---
sci-biology/argo-bin/argo-bin-1.0.31.ebuild | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
diff --git a/sci-biology/argo-bin/argo-bin-1.0.31.ebuild b/sci-biology/argo-bin/argo-bin-1.0.31.ebuild
index ee72f80..0a1f7aa 100644
--- a/sci-biology/argo-bin/argo-bin-1.0.31.ebuild
+++ b/sci-biology/argo-bin/argo-bin-1.0.31.ebuild
@@ -4,7 +4,7 @@
EAPI=3
-inherit toolchain-funcs java-utils-2
+inherit java-utils-2 toolchain-funcs
DESCRIPTION="The Argo Genome Browser is a production tool for
visualizing and manually annotating whole genomes
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/argo-bin/
@ 2011-06-25 17:22 Justin Lecher
0 siblings, 0 replies; 6+ messages in thread
From: Justin Lecher @ 2011-06-25 17:22 UTC (permalink / raw
To: gentoo-commits
commit: a05c12479748b40d35fbddfe85904dc953177517
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jun 25 14:24:23 2011 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jun 25 14:24:23 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a05c1247
Cleaned ebuild
(Portage version: 2.2.0_alpha41/git/Linux x86_64, signed Manifest commit with key 70EB7916)
---
sci-biology/argo-bin/ChangeLog | 7 +++++++
sci-biology/argo-bin/argo-bin-1.0.31.ebuild | 9 +++------
2 files changed, 10 insertions(+), 6 deletions(-)
diff --git a/sci-biology/argo-bin/ChangeLog b/sci-biology/argo-bin/ChangeLog
new file mode 100644
index 0000000..7f9152a
--- /dev/null
+++ b/sci-biology/argo-bin/ChangeLog
@@ -0,0 +1,7 @@
+# ChangeLog for sci-biology/argo-bin
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 25 Jun 2011; Justin Lecher <jlec@gentoo.org> argo-bin-1.0.31.ebuild:
+ Cleaned ebuild
+
diff --git a/sci-biology/argo-bin/argo-bin-1.0.31.ebuild b/sci-biology/argo-bin/argo-bin-1.0.31.ebuild
index 0a1f7aa..7ed58fa 100644
--- a/sci-biology/argo-bin/argo-bin-1.0.31.ebuild
+++ b/sci-biology/argo-bin/argo-bin-1.0.31.ebuild
@@ -1,14 +1,12 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2011 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-19-r2.ebuild,v 1.2 2010/10/10 21:20:04 ulm Exp $
-EAPI=3
+EAPI=4
inherit java-utils-2 toolchain-funcs
-DESCRIPTION="The Argo Genome Browser is a production tool for
- visualizing and manually annotating whole genomes
- stored in .gff3 files"
+DESCRIPTION="Visualization and manually annotating whole genomes"
HOMEPAGE="http://www.broadinstitute.org/annotation/argo/"
SRC_URI="http://www.broadinstitute.org/annotation/argo/argo.jar"
#SRC_URI="http://www.broadinstitute.org/annotation/argo/src/workspace-2008-03-11.tgz"
@@ -26,4 +24,3 @@ src_install() {
java-pkg_newjar "${DISTDIR}"/argo.jar argo.jar
java-pkg_dolauncher
}
-
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/argo-bin/
@ 2015-05-25 18:59 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2015-05-25 18:59 UTC (permalink / raw
To: gentoo-commits
commit: ffdec8d98b9e7e5302043aedd22f44b1e631011c
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon May 25 18:59:01 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon May 25 18:59:01 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ffdec8d9
sci-biology/argo-bin: redefine S variable so we can chdir to a WORKDIR (not sure why the jar archive must be unpacked there at all ...)
Package-Manager: portage-2.2.18
sci-biology/argo-bin/ChangeLog | 8 ++++++--
sci-biology/argo-bin/argo-bin-1.0.31.ebuild | 4 +++-
2 files changed, 9 insertions(+), 3 deletions(-)
diff --git a/sci-biology/argo-bin/ChangeLog b/sci-biology/argo-bin/ChangeLog
index 7f9152a..d8c050f 100644
--- a/sci-biology/argo-bin/ChangeLog
+++ b/sci-biology/argo-bin/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-biology/argo-bin
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ argo-bin-1.0.31.ebuild:
+ sci-biology/argo-bin: redefine S variable so we can chdir to a WORKDIR (not
+ sure why the jar archive must be unpacked there at all ...)
+
25 Jun 2011; Justin Lecher <jlec@gentoo.org> argo-bin-1.0.31.ebuild:
Cleaned ebuild
-
diff --git a/sci-biology/argo-bin/argo-bin-1.0.31.ebuild b/sci-biology/argo-bin/argo-bin-1.0.31.ebuild
index 6a708d5..6db9160 100644
--- a/sci-biology/argo-bin/argo-bin-1.0.31.ebuild
+++ b/sci-biology/argo-bin/argo-bin-1.0.31.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: $
@@ -20,6 +20,8 @@ DEPEND=""
RDEPEND="${DEPEND}
java? ( >=virtual/jre-1.4 )"
+S="${WORKDIR}"
+
src_install() {
java-pkg_newjar "${DISTDIR}"/argo.jar argo.jar
java-pkg_dolauncher
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/argo-bin/
@ 2015-05-26 9:26 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2015-05-26 9:26 UTC (permalink / raw
To: gentoo-commits
commit: caf6cafd3614ade1e427bb619a9c7cd61faee579
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue May 26 09:25:38 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue May 26 09:25:38 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=caf6cafd
sci-biology/argo-bin: ebuild cleanup; version bump
Package-Manager: portage-2.2.18
sci-biology/argo-bin/ChangeLog | 6 ++++++
sci-biology/argo-bin/argo-bin-1.0.31.ebuild | 13 ++++++++-----
.../{argo-bin-1.0.31.ebuild => argo-bin-2.0.3.ebuild} | 17 ++++++++++-------
3 files changed, 24 insertions(+), 12 deletions(-)
diff --git a/sci-biology/argo-bin/ChangeLog b/sci-biology/argo-bin/ChangeLog
index d8c050f..01ad496 100644
--- a/sci-biology/argo-bin/ChangeLog
+++ b/sci-biology/argo-bin/ChangeLog
@@ -2,6 +2,12 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*argo-bin-2.0.3 (26 May 2015)
+
+ 26 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +argo-bin-2.0.3.ebuild, argo-bin-1.0.31.ebuild:
+ sci-biology/argo-bin: ebuild cleanup; version bump
+
25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
argo-bin-1.0.31.ebuild:
sci-biology/argo-bin: redefine S variable so we can chdir to a WORKDIR (not
diff --git a/sci-biology/argo-bin/argo-bin-1.0.31.ebuild b/sci-biology/argo-bin/argo-bin-1.0.31.ebuild
index 6db9160..db8efaf 100644
--- a/sci-biology/argo-bin/argo-bin-1.0.31.ebuild
+++ b/sci-biology/argo-bin/argo-bin-1.0.31.ebuild
@@ -2,23 +2,26 @@
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=4
+EAPI=5
inherit java-utils-2 toolchain-funcs
DESCRIPTION="Visualization and manually annotating whole genomes"
-HOMEPAGE="http://www.broadinstitute.org/annotation/argo/"
+HOMEPAGE="http://www.broadinstitute.org/annotation/argo2
+ http://www.broadinstitute.org/annotation/argo"
SRC_URI="http://www.broadinstitute.org/annotation/argo/argo.jar"
-#SRC_URI="http://www.broadinstitute.org/annotation/argo/src/workspace-2008-03-11.tgz"
+#
+# Release Number: 1.0.31
+# Release Date: 2010-02-05
LICENSE="LGPL-3"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="java"
-DEPEND=""
+DEPEND="!sci-biology/argo"
RDEPEND="${DEPEND}
- java? ( >=virtual/jre-1.4 )"
+ java? ( >=virtual/jre-1.5:* )"
S="${WORKDIR}"
diff --git a/sci-biology/argo-bin/argo-bin-1.0.31.ebuild b/sci-biology/argo-bin/argo-bin-2.0.3.ebuild
similarity index 51%
copy from sci-biology/argo-bin/argo-bin-1.0.31.ebuild
copy to sci-biology/argo-bin/argo-bin-2.0.3.ebuild
index 6db9160..5659a97 100644
--- a/sci-biology/argo-bin/argo-bin-1.0.31.ebuild
+++ b/sci-biology/argo-bin/argo-bin-2.0.3.ebuild
@@ -2,27 +2,30 @@
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=4
+EAPI=5
inherit java-utils-2 toolchain-funcs
DESCRIPTION="Visualization and manually annotating whole genomes"
-HOMEPAGE="http://www.broadinstitute.org/annotation/argo/"
-SRC_URI="http://www.broadinstitute.org/annotation/argo/argo.jar"
-#SRC_URI="http://www.broadinstitute.org/annotation/argo/src/workspace-2008-03-11.tgz"
+HOMEPAGE="http://www.broadinstitute.org/annotation/argo2
+ http://www.broadinstitute.org/annotation/argo"
+SRC_URI="http://www.broadinstitute.org/annotation/argo2/releases/argo2.jar"
+#
+# Release Number: 3
+# Release Date: 2010-06-23
LICENSE="LGPL-3"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="java"
-DEPEND=""
+DEPEND="!sci-biology/argo"
RDEPEND="${DEPEND}
- java? ( >=virtual/jre-1.4 )"
+ java? ( >=virtual/jre-1.5:* )"
S="${WORKDIR}"
src_install() {
- java-pkg_newjar "${DISTDIR}"/argo.jar argo.jar
+ java-pkg_newjar "${DISTDIR}"/argo2.jar argo2.jar
java-pkg_dolauncher
}
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/argo-bin/
@ 2015-05-26 9:38 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2015-05-26 9:38 UTC (permalink / raw
To: gentoo-commits
commit: 020c48a333f16ea10caa4f66cfc955de7c162f90
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue May 26 09:37:43 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue May 26 09:37:43 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=020c48a3
sci-biology/argo-bin: remove IUSE
Package-Manager: portage-2.2.18
sci-biology/argo-bin/ChangeLog | 4 ++++
sci-biology/argo-bin/argo-bin-1.0.31.ebuild | 5 ++---
sci-biology/argo-bin/argo-bin-2.0.3.ebuild | 5 ++---
3 files changed, 8 insertions(+), 6 deletions(-)
diff --git a/sci-biology/argo-bin/ChangeLog b/sci-biology/argo-bin/ChangeLog
index 01ad496..1bf8c1a 100644
--- a/sci-biology/argo-bin/ChangeLog
+++ b/sci-biology/argo-bin/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 26 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ argo-bin-1.0.31.ebuild, argo-bin-2.0.3.ebuild:
+ sci-biology/argo-bin: remove IUSE
+
*argo-bin-2.0.3 (26 May 2015)
26 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/argo-bin/argo-bin-1.0.31.ebuild b/sci-biology/argo-bin/argo-bin-1.0.31.ebuild
index db8efaf..a59ae7a 100644
--- a/sci-biology/argo-bin/argo-bin-1.0.31.ebuild
+++ b/sci-biology/argo-bin/argo-bin-1.0.31.ebuild
@@ -17,12 +17,11 @@ SRC_URI="http://www.broadinstitute.org/annotation/argo/argo.jar"
LICENSE="LGPL-3"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE="java"
+IUSE=""
DEPEND="!sci-biology/argo"
RDEPEND="${DEPEND}
- java? ( >=virtual/jre-1.5:* )"
-
+ >=virtual/jre-1.5:*"
S="${WORKDIR}"
src_install() {
diff --git a/sci-biology/argo-bin/argo-bin-2.0.3.ebuild b/sci-biology/argo-bin/argo-bin-2.0.3.ebuild
index 5659a97..8e475e6 100644
--- a/sci-biology/argo-bin/argo-bin-2.0.3.ebuild
+++ b/sci-biology/argo-bin/argo-bin-2.0.3.ebuild
@@ -17,12 +17,11 @@ SRC_URI="http://www.broadinstitute.org/annotation/argo2/releases/argo2.jar"
LICENSE="LGPL-3"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE="java"
+IUSE=""
DEPEND="!sci-biology/argo"
RDEPEND="${DEPEND}
- java? ( >=virtual/jre-1.5:* )"
-
+ >=virtual/jre-1.5:*"
S="${WORKDIR}"
src_install() {
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/argo-bin/
@ 2021-01-13 21:06 Andrew Ammerlaan
0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2021-01-13 21:06 UTC (permalink / raw
To: gentoo-commits
commit: ccf1df8eed92e36f75be2e7a3bea8532950c3602
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Wed Jan 13 20:42:31 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Wed Jan 13 20:42:31 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ccf1df8e
sci-biology/argo-bin: use https for homepage
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/argo-bin/argo-bin-1.0.31.ebuild | 8 ++++----
sci-biology/argo-bin/argo-bin-2.0.3.ebuild | 8 ++++----
2 files changed, 8 insertions(+), 8 deletions(-)
diff --git a/sci-biology/argo-bin/argo-bin-1.0.31.ebuild b/sci-biology/argo-bin/argo-bin-1.0.31.ebuild
index 5f0fae0dc..615c186b2 100644
--- a/sci-biology/argo-bin/argo-bin-1.0.31.ebuild
+++ b/sci-biology/argo-bin/argo-bin-1.0.31.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -6,9 +6,9 @@ EAPI=5
inherit java-utils-2 toolchain-funcs
DESCRIPTION="Visualization and manually annotating whole genomes"
-HOMEPAGE="http://www.broadinstitute.org/annotation/argo2
- http://www.broadinstitute.org/annotation/argo"
-SRC_URI="http://www.broadinstitute.org/annotation/argo/argo.jar"
+HOMEPAGE="https://www.broadinstitute.org/annotation/argo2
+ https://www.broadinstitute.org/annotation/argo"
+SRC_URI="https://www.broadinstitute.org/annotation/argo/argo.jar"
#
# Release Number: 1.0.31
# Release Date: 2010-02-05
diff --git a/sci-biology/argo-bin/argo-bin-2.0.3.ebuild b/sci-biology/argo-bin/argo-bin-2.0.3.ebuild
index 7a6547fb8..8b07ccaaa 100644
--- a/sci-biology/argo-bin/argo-bin-2.0.3.ebuild
+++ b/sci-biology/argo-bin/argo-bin-2.0.3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -6,9 +6,9 @@ EAPI=5
inherit java-utils-2 toolchain-funcs
DESCRIPTION="Visualization and manually annotating whole genomes"
-HOMEPAGE="http://www.broadinstitute.org/annotation/argo2
- http://www.broadinstitute.org/annotation/argo"
-SRC_URI="http://www.broadinstitute.org/annotation/argo2/releases/argo2.jar"
+HOMEPAGE="https://www.broadinstitute.org/annotation/argo2
+ https://www.broadinstitute.org/annotation/argo"
+SRC_URI="https://www.broadinstitute.org/annotation/argo2/releases/argo2.jar"
#
# Release Number: 3
# Release Date: 2010-06-23
^ permalink raw reply related [flat|nested] 6+ messages in thread
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