* [gentoo-commits] proj/sci:master commit in: sci-biology/manatee-jcvi/
@ 2013-08-29 14:28 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2013-08-29 14:28 UTC (permalink / raw
To: gentoo-commits
commit: 101952a9d415206f8f45d06e6f51f277fdf38621
Author: Martin Mokrejš <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Thu Aug 29 14:27:51 2013 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Aug 29 14:27:51 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=101952a9
pushing out a draft ebuild from manatee-jcvi
---
sci-biology/manatee-jcvi/ChangeLog | 11 +++++
sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild | 53 ++++++++++++++++++++++
sci-biology/manatee-jcvi/metadata.xml | 9 ++++
3 files changed, 73 insertions(+)
diff --git a/sci-biology/manatee-jcvi/ChangeLog b/sci-biology/manatee-jcvi/ChangeLog
new file mode 100644
index 0000000..ab9e1df
--- /dev/null
+++ b/sci-biology/manatee-jcvi/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-biology/manatee-jcvi
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*manatee-jcvi-2.4.3 (29 Aug 2013)
+
+ 29 Aug 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +manatee-jcvi-2.4.3.ebuild, +metadata.xml:
+ Initial ebuild for the other version of manatee, using different database
+ schema.
+
diff --git a/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild b/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild
new file mode 100644
index 0000000..abc3874
--- /dev/null
+++ b/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild
@@ -0,0 +1,53 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+DESCRIPTION="A JCVI version of Manatee: a genome annotation tool that can view, modify, and store annotation for prokaryotic and eukaryotic genomes."
+HOMEPAGE="http://manatee.sourceforge.net/jcvi/downloads.shtml"
+SRC_URI="http://downloads.sourceforge.net/project/manatee/manatee/manatee-2.4.3/manatee-2.4.3.tgz"
+
+LICENSE="Artistic-Manatee"
+SLOT="0"
+KEYWORDS=""
+#KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=">=dev-libs/expat-1.95.8
+ >=media-libs/gd-2.0.34
+ dev-perl/CGI
+ dev-perl/CGI-Carp
+ dev-perl/CGI-Cookie
+ dev-perl/DBI
+ dev-perl/DBD-mysql
+ dev-perl/XML-Parser
+ dev-perl/XML-Twig
+ dev-perl/XML-Simple
+ dev-perl/XML-Writer
+ dev-perl/HTML-Template
+ dev-perl/Tree-DAG_Node
+ dev-perl/File-Spec
+ dev-perl/Data-Dumper
+ dev-perl/GD
+ dev-perl/GD-Text
+ dev-perl/GD-Graph
+ dev-perl/Storable
+ dev-perl/Log-Log4perl
+ dev-perl/Log-Cabin
+ dev-perl/Date-Manip
+ dev-perl/IO-Tee
+ dev-perl/MLDBM"
+RDEPEND="${DEPEND}
+ >=dev-db/mysql-5.0
+ >=www-servers/apache-2.2"
+
+S="${WORKDIR}"/manatee-"${PV}"
+
+src_configure(){
+ econf HTTPD=/usr/sbin/httpd HTTPD_SCRIPT_HOME=/var/www/cgi-bin HTTPD_DOC_HOME=/var/www/htdocs MYSQLD=/usr/sbin/mysqld || die
+}
+
+src_compile(){
+ emake || die
+}
diff --git a/sci-biology/manatee-jcvi/metadata.xml b/sci-biology/manatee-jcvi/metadata.xml
new file mode 100644
index 0000000..07b5255
--- /dev/null
+++ b/sci-biology/manatee-jcvi/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/manatee-jcvi/
@ 2014-09-16 17:50 Christoph Junghans
0 siblings, 0 replies; 6+ messages in thread
From: Christoph Junghans @ 2014-09-16 17:50 UTC (permalink / raw
To: gentoo-commits
commit: b53aea0d3fed2eb6dadf7513bd232a58a871316d
Author: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 16 17:45:16 2014 +0000
Commit: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Sep 16 17:45:16 2014 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b53aea0d
clean up
Package-Manager: portage-2.2.8-r1
---
sci-biology/manatee-jcvi/ChangeLog | 6 +++--
sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild | 26 +++++++++++-----------
2 files changed, 17 insertions(+), 15 deletions(-)
diff --git a/sci-biology/manatee-jcvi/ChangeLog b/sci-biology/manatee-jcvi/ChangeLog
index ab9e1df..71bda27 100644
--- a/sci-biology/manatee-jcvi/ChangeLog
+++ b/sci-biology/manatee-jcvi/ChangeLog
@@ -1,11 +1,13 @@
# ChangeLog for sci-biology/manatee-jcvi
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> manatee-jcvi-2.4.3.ebuild:
+ clean up
+
*manatee-jcvi-2.4.3 (29 Aug 2013)
29 Aug 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+manatee-jcvi-2.4.3.ebuild, +metadata.xml:
Initial ebuild for the other version of manatee, using different database
schema.
-
diff --git a/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild b/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild
index c04c5fa..7eec8b2 100644
--- a/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild
+++ b/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild
@@ -2,9 +2,9 @@
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=3
+EAPI=5
-DESCRIPTION="A JCVI version of Manatee: a genome annotation tool that can view, modify, and store annotation for prokaryotic and eukaryotic genomes."
+DESCRIPTION="genome annotation tool: view, modify, and store annotation for prokaryotic and eukaryotic genomes."
HOMEPAGE="http://manatee.sourceforge.net/jcvi/downloads.shtml"
SRC_URI="http://downloads.sourceforge.net/project/manatee/manatee/manatee-2.4.3/manatee-2.4.3.tgz"
@@ -16,9 +16,6 @@ IUSE=""
DEPEND=">=dev-libs/expat-1.95.8
>=media-libs/gd-2.0.34
- dev-perl/CGI
- dev-perl/CGI-Carp
- dev-perl/CGI-Cookie
dev-perl/DBI
dev-perl/DBD-mysql
dev-perl/XML-Parser
@@ -27,17 +24,20 @@ DEPEND=">=dev-libs/expat-1.95.8
dev-perl/XML-Writer
dev-perl/HTML-Template
dev-perl/Tree-DAG_Node
- dev-perl/File-Spec
- dev-perl/Data-Dumper
+ perl-core/File-Spec
+ perl-core/Data-Dumper
dev-perl/GD
- dev-perl/GD-Text
- dev-perl/GD-Graph
- dev-perl/Storable
+ perl-core/Storable
dev-perl/Log-Log4perl
dev-perl/Log-Cabin
- dev-perl/Date-Manip
dev-perl/IO-Tee
dev-perl/MLDBM"
+ #dev-perl/CGI
+ #dev-perl/CGI-Carp
+ #dev-perl/CGI-Cookie
+ #dev-perl/GD-Text
+ #dev-perl/GD-Graph
+ #dev-perl/Date-Manip
RDEPEND="${DEPEND}
>=dev-db/mysql-5.0
>=www-servers/apache-2.2"
@@ -45,9 +45,9 @@ RDEPEND="${DEPEND}
S="${WORKDIR}"/manatee-"${PV}"
src_configure(){
- econf HTTPD=/usr/sbin/httpd HTTPD_SCRIPT_HOME=/var/www/cgi-bin HTTPD_DOC_HOME=/var/www/htdocs MYSQLD=/usr/sbin/mysqld || die
+ econf HTTPD=/usr/sbin/httpd HTTPD_SCRIPT_HOME=/var/www/cgi-bin HTTPD_DOC_HOME=/var/www/htdocs MYSQLD=/usr/sbin/mysqld
}
src_compile(){
- emake || die
+ emake
}
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/manatee-jcvi/
@ 2014-11-13 13:00 Justin Lecher
0 siblings, 0 replies; 6+ messages in thread
From: Justin Lecher @ 2014-11-13 13:00 UTC (permalink / raw
To: gentoo-commits
commit: 6a72d5353bf00132ba76cde0c05003f065222fae
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Nov 13 12:57:49 2014 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Nov 13 12:57:49 2014 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6a72d535
sci-biology/manatee-jcvi: Use perl virtuals instead of core
Package-Manager: portage-2.2.14
---
sci-biology/manatee-jcvi/ChangeLog | 4 ++++
sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild | 6 +++---
sci-biology/manatee-jcvi/metadata.xml | 10 +++++-----
3 files changed, 12 insertions(+), 8 deletions(-)
diff --git a/sci-biology/manatee-jcvi/ChangeLog b/sci-biology/manatee-jcvi/ChangeLog
index 71bda27..da85159 100644
--- a/sci-biology/manatee-jcvi/ChangeLog
+++ b/sci-biology/manatee-jcvi/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 13 Nov 2014; Justin Lecher <jlec@gentoo.org> manatee-jcvi-2.4.3.ebuild,
+ metadata.xml:
+ Use perl virtuals instead of core
+
16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> manatee-jcvi-2.4.3.ebuild:
clean up
diff --git a/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild b/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild
index 7eec8b2..08ec387 100644
--- a/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild
+++ b/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild
@@ -24,10 +24,10 @@ DEPEND=">=dev-libs/expat-1.95.8
dev-perl/XML-Writer
dev-perl/HTML-Template
dev-perl/Tree-DAG_Node
- perl-core/File-Spec
- perl-core/Data-Dumper
+ virtual/perl-File-Spec
+ virtual/perl-Data-Dumper
dev-perl/GD
- perl-core/Storable
+ virtual/perl-Storable
dev-perl/Log-Log4perl
dev-perl/Log-Cabin
dev-perl/IO-Tee
diff --git a/sci-biology/manatee-jcvi/metadata.xml b/sci-biology/manatee-jcvi/metadata.xml
index 07b5255..2bc8930 100644
--- a/sci-biology/manatee-jcvi/metadata.xml
+++ b/sci-biology/manatee-jcvi/metadata.xml
@@ -1,9 +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>
+ <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/manatee-jcvi/
@ 2015-10-27 9:55 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2015-10-27 9:55 UTC (permalink / raw
To: gentoo-commits
commit: 706be1134587796b51b6fdde585d3b5a3fdf0209
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Oct 27 09:54:01 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Oct 27 09:54:01 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=706be113
sci-biology/manatee-jcvi: depend virtual/mysql
Package-Manager: portage-2.2.18
sci-biology/manatee-jcvi/ChangeLog | 6 +++++-
sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild | 4 ++--
2 files changed, 7 insertions(+), 3 deletions(-)
diff --git a/sci-biology/manatee-jcvi/ChangeLog b/sci-biology/manatee-jcvi/ChangeLog
index 51f8c4e..503585b 100644
--- a/sci-biology/manatee-jcvi/ChangeLog
+++ b/sci-biology/manatee-jcvi/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-biology/manatee-jcvi
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Id$
+ 27 Oct 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ manatee-jcvi-2.4.3.ebuild:
+ sci-biology/manatee-jcvi: depend virtual/mysql
+
13 Nov 2014; Justin Lecher <jlec@gentoo.org> manatee-jcvi-2.4.3.ebuild,
metadata.xml:
Use perl virtuals instead of core
diff --git a/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild b/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild
index a372621..5701bb8 100644
--- a/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild
+++ b/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.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
# $Id$
@@ -39,7 +39,7 @@ DEPEND=">=dev-libs/expat-1.95.8
#dev-perl/GD-Graph
#dev-perl/Date-Manip
RDEPEND="${DEPEND}
- >=dev-db/mysql-5.0
+ >=virtual/mysql-5:*
>=www-servers/apache-2.2"
S="${WORKDIR}"/manatee-"${PV}"
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/manatee-jcvi/
@ 2021-01-19 12:18 Andrew Ammerlaan
0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2021-01-19 12:18 UTC (permalink / raw
To: gentoo-commits
commit: 33859d0cc113b0030567ae7b0f0cc6d6574ae08c
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 12:17:40 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 12:17:40 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=33859d0c
sci-biology/manatee-jcvi: EAPi bump. fix fetch
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild | 8 +++-----
1 file changed, 3 insertions(+), 5 deletions(-)
diff --git a/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild b/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild
index 344f3b59b..9536b2664 100644
--- a/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild
+++ b/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild
@@ -1,17 +1,15 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
DESCRIPTION="Genome annotation tool"
HOMEPAGE="http://manatee.sourceforge.net/jcvi/downloads.shtml"
-SRC_URI="http://downloads.sourceforge.net/project/manatee/manatee/manatee-2.4.3/manatee-2.4.3.tgz"
+SRC_URI="http://downloads.sourceforge.net/project/manatee/manatee/manatee-${PV}/manatee-2.4.3.tgz"
LICENSE="Artistic-Manatee"
SLOT="0"
KEYWORDS=""
-#KEYWORDS="~amd64 ~x86"
-IUSE=""
DEPEND=">=dev-libs/expat-1.95.8
>=media-libs/gd-2.0.34
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/manatee-jcvi/
@ 2021-02-01 11:29 Andrew Ammerlaan
0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2021-02-01 11:29 UTC (permalink / raw
To: gentoo-commits
commit: e9c4828c371a3795943c5ae94f403e464714e56d
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Feb 1 11:28:57 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Feb 1 11:28:57 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e9c4828c
sci-biology/manatee-jcvi: add some missing deps
Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild | 22 +++++++++++++---------
1 file changed, 13 insertions(+), 9 deletions(-)
diff --git a/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild b/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild
index 9536b2664..7bc28decf 100644
--- a/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild
+++ b/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild
@@ -28,16 +28,20 @@ DEPEND=">=dev-libs/expat-1.95.8
dev-perl/Log-Log4perl
dev-perl/Log-Cabin
dev-perl/IO-Tee
- dev-perl/MLDBM"
- #dev-perl/CGI
- #dev-perl/CGI-Carp
- #dev-perl/CGI-Cookie
- #dev-perl/GD-Text
- #dev-perl/GD-Graph
- #dev-perl/Date-Manip
+ dev-perl/MLDBM
+ dev-perl/CGI
+ dev-perl/DBI
+ dev-perl/Apache-DBI
+ dev-perl/Date-Manip
+"
+# dev-perl/CGI-Carp
+# dev-perl/CGI-Cookie
+# dev-perl/GD-Text
+# dev-perl/GD-Graph
+#
RDEPEND="${DEPEND}
- >=virtual/mysql-5:*
- >=www-servers/apache-2.2"
+ >=virtual/mysql-5:*
+ >=www-servers/apache-2.2"
S="${WORKDIR}"/manatee-"${PV}"
^ permalink raw reply related [flat|nested] 6+ messages in thread
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