* [gentoo-commits] proj/sci:master commit in: sci-biology/gbrowse/
@ 2011-06-25 17:22 Justin Lecher
0 siblings, 0 replies; 9+ messages in thread
From: Justin Lecher @ 2011-06-25 17:22 UTC (permalink / raw
To: gentoo-commits
commit: c051a8f8d54dd27ef4247923cc4fec182b6548df
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jun 25 14:29:32 2011 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jun 25 14:29:32 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c051a8f8
Cleaned ebuild, 'http://search.cpan.org/CPAN' found in thirdpartymirrors
(Portage version: 2.2.0_alpha41/git/Linux x86_64, signed Manifest commit with key 70EB7916)
---
sci-biology/gbrowse/ChangeLog | 8 +++-
sci-biology/gbrowse/gbrowse-1.70.ebuild | 68 ---------------------------
sci-biology/gbrowse/gbrowse-2.00.ebuild | 76 -------------------------------
sci-biology/gbrowse/gbrowse-2.26.ebuild | 33 +++++++------
sci-biology/gbrowse/gbrowse-2.33.ebuild | 33 +++++++-------
5 files changed, 41 insertions(+), 177 deletions(-)
diff --git a/sci-biology/gbrowse/ChangeLog b/sci-biology/gbrowse/ChangeLog
index 8024f81..b66d69a 100644
--- a/sci-biology/gbrowse/ChangeLog
+++ b/sci-biology/gbrowse/ChangeLog
@@ -1,7 +1,11 @@
-# ChangeLog for sci-biology/generic-genome-browser
-# Copyright 2000-2010 Gentoo Foundation; Distributed under the GPL v2
+# ChangeLog for sci-biology/gbrowse
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/generic-genome-browser/ChangeLog,v 1.10 2007/07/29 17:07:38 phreak Exp $
+ 25 Jun 2011; Justin Lecher <jlec@gentoo.org> -gbrowse-1.70.ebuild,
+ -gbrowse-2.00.ebuild, gbrowse-2.26.ebuild, gbrowse-2.33.ebuild:
+ Cleaned ebuild, 'http://search.cpan.org/CPAN' found in thirdpartymirrors
+
05 Feb 2010; Andrey Kislyuk <weaver@gentoo.org> ChangeLog:
Version bump
diff --git a/sci-biology/gbrowse/gbrowse-1.70.ebuild b/sci-biology/gbrowse/gbrowse-1.70.ebuild
deleted file mode 100644
index 9bf0f47..0000000
--- a/sci-biology/gbrowse/gbrowse-1.70.ebuild
+++ /dev/null
@@ -1,68 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/generic-genome-browser/generic-genome-browser-1.58.ebuild,v 1.9 2007/07/29 17:07:38 phreak Exp $
-
-EAPI="2"
-
-inherit perl-module webapp
-
-MY_P="Generic-Genome-Browser-${PV}"
-
-DESCRIPTION="The generic genome browser provides a display of genomic annotations on interactive web pages"
-HOMEPAGE="http://gmod.org"
-SRC_URI="mirror://sourceforge/gmod/${MY_P}.tar.gz"
-
-LICENSE="Artistic"
-# webapp ebuilds do not set SLOT
-KEYWORDS="~x86 ~amd64"
-IUSE="-minimal" # lwp moby scf
-
-S="${WORKDIR}/${MY_P}"
-
-# TODO: dev-perl/MOBY, dev-perl/Bio-SCF, dev-perl/libwww-perl, LWP
-DEPEND=">=dev-lang/perl-5.8.8
- >=sci-biology/bioperl-1.6
- >=dev-perl/GD-2.07
- dev-perl/IO-String
- virtual/perl-Digest-MD5
- >=dev-perl/CGI-Session-4.03
- dev-perl/Statistics-Descriptive
- >=dev-perl/Bio-Graphics-1.97"
-RDEPEND="${DEPEND}
- >=www-servers/apache-2.0.47
- >=virtual/perl-CGI-2.56
- dev-perl/DBI
- dev-perl/DBD-mysql
- dev-perl/Class-Base
- dev-perl/Text-Shellwords
- !minimal? (
- dev-perl/XML-Parser
- dev-perl/XML-Writer
- dev-perl/XML-Twig
- dev-perl/XML-DOM
- dev-perl/GD-SVG
- dev-perl/Bio-Das
- )"
-
-src_configure() {
- webapp_src_preinst
- perl Makefile.PL \
- HTDOCS="${D}/${MY_HTDOCSDIR}" \
- CGIBIN="${D}/${MY_HTDOCSDIR}/cgi-bin" \
- CONF="${D}/etc" \
- PREFIX="${D}/usr" \
- PACKAGE_DIR="${D}" \
- INSTALLDIRS=vendor \
- GBROWSE_ROOT=gbrowse \
- DESTDIR="${ROOT}" \
- || die
-}
-
-src_install() {
- mydoc="Changes README TODO INSTALL"
- perl-module_src_install
-
- # TODO: write our own readme
- webapp_postinst_txt en "${S}/INSTALL"
- webapp_src_install
-}
diff --git a/sci-biology/gbrowse/gbrowse-2.00.ebuild b/sci-biology/gbrowse/gbrowse-2.00.ebuild
deleted file mode 100644
index cce42a3..0000000
--- a/sci-biology/gbrowse/gbrowse-2.00.ebuild
+++ /dev/null
@@ -1,76 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/generic-genome-browser/generic-genome-browser-1.58.ebuild,v 1.9 2007/07/29 17:07:38 phreak Exp $
-
-EAPI="2"
-
-inherit perl-module webapp
-
-MY_P="GBrowse-${PV}"
-
-DESCRIPTION="The generic genome browser provides a display of genomic annotations on interactive web pages"
-HOMEPAGE="http://gmod.org"
-SRC_URI="mirror://sourceforge/gmod/${MY_P}.tar.gz"
-
-LICENSE="Artistic"
-# webapp ebuilds do not set SLOT
-KEYWORDS="~x86 ~amd64"
-IUSE="-minimal" # lwp moby scf
-
-S="${WORKDIR}/${MY_P}"
-
-# TODO: dev-perl/MOBY, dev-perl/Bio-SCF, dev-perl/Safe-World (not compatible w/perl-5.10)
-DEPEND=">=dev-lang/perl-5.8.8
- >=sci-biology/bioperl-1.6
- >=dev-perl/GD-2.07
- dev-perl/IO-String
- virtual/perl-Digest-MD5
- >=dev-perl/CGI-Session-4.03
- dev-perl/Statistics-Descriptive
- >=dev-perl/Bio-Graphics-1.97
- dev-perl/JSON
- dev-perl/libwww-perl"
-RDEPEND="${DEPEND}
- >=www-servers/apache-2.0.47
- dev-perl/DBI
- || ( dev-perl/DBD-Pg dev-perl/DBD-mysql )
- !minimal? (
- dev-perl/File-NFSLock
- dev-perl/FCGI
- perl-core/Math-BigInt
- dev-perl/Digest-SHA1
- dev-perl/Crypt-SSLeay
- dev-perl/Net-SMTP-SSL
- dev-perl/GD-SVG
- dev-perl/Net-OpenID-Consumer
- virtual/perl-DB_File
- dev-perl/DB_File-Lock
- )"
-
-src_prepare() {
- sed -i 's/return unless -t STDIN/return/' install_util/GBrowseInstall.pm || die
-}
-
-src_configure() {
- webapp_src_preinst
- perl Makefile.PL \
- HTDOCS="${D}/${MY_HTDOCSDIR}" \
- CGIBIN="${D}/${MY_HTDOCSDIR}/cgi-bin" \
- CONF="${D}/etc" \
- PREFIX="${D}/usr" \
- PACKAGE_DIR="${D}" \
- INSTALLDIRS=vendor \
- GBROWSE_ROOT=gbrowse \
- DESTDIR="${ROOT}" \
- || die
-}
-
-src_install() {
- mydoc="Changes README TODO INSTALL"
- perl-module_src_install
-
- # TODO: write our own readme
- webapp_postinst_txt en "${S}/INSTALL"
- webapp_src_install
-# find "${D}" -type f | xargs sed -i "s|${D}||" || die
-}
diff --git a/sci-biology/gbrowse/gbrowse-2.26.ebuild b/sci-biology/gbrowse/gbrowse-2.26.ebuild
index 89000cf..363d18d 100644
--- a/sci-biology/gbrowse/gbrowse-2.26.ebuild
+++ b/sci-biology/gbrowse/gbrowse-2.26.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2011 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
EAPI="2"
@@ -7,19 +7,21 @@ inherit perl-module webapp
MY_P="GBrowse-${PV}"
-DESCRIPTION="The generic genome browser provides a display of genomic annotations on interactive web pages"
-HOMEPAGE="http://gmod.org"
-SRC_URI="mirror://sourceforge/gmod/${MY_P}.tar.gz
- test? ( http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/saccharomyces_cerevisiae.gff.bz2
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/Refseq_Genome_TBLASTX.tar.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/README-gff-files
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/human.gff.tar.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.fasta.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.gff.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.fasta.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.gff.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.fasta.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.gff.gz )"
+DESCRIPTION="Display of genomic annotations on interactive web pages"
+HOMEPAGE="http://gmod.org/"
+SRC_URI="
+ mirror://sourceforge/gmod/${MY_P}.tar.gz
+ test? (
+ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/saccharomyces_cerevisiae.gff.bz2
+ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/Refseq_Genome_TBLASTX.tar.gz
+ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/README-gff-files
+ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/human.gff.tar.gz
+ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.fasta.gz
+ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.gff.gz
+ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.fasta.gz
+ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.gff.gz
+ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.fasta.gz
+ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.gff.gz )"
LICENSE="Artistic"
# webapp ebuilds do not set SLOT
@@ -30,7 +32,8 @@ S="${WORKDIR}/${MY_P}"
# TODO: dev-perl/MOBY, dev-perl/Bio-SCF, dev-perl/Safe-World (not compatible w/perl-5.10)
# TODO: make sure www-servers/apache +cgi
-DEPEND=">=dev-lang/perl-5.8.8
+DEPEND="
+ >=dev-lang/perl-5.8.8
dev-perl/Capture-Tiny
>=sci-biology/bioperl-1.6
>=dev-perl/GD-2.07
diff --git a/sci-biology/gbrowse/gbrowse-2.33.ebuild b/sci-biology/gbrowse/gbrowse-2.33.ebuild
index e2bcfc3..9cc3ce4 100644
--- a/sci-biology/gbrowse/gbrowse-2.33.ebuild
+++ b/sci-biology/gbrowse/gbrowse-2.33.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2011 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
EAPI="2"
@@ -7,21 +7,23 @@ inherit perl-module webapp
MY_P="GBrowse-${PV}"
-DESCRIPTION="The generic genome browser provides a display of genomic annotations on interactive web pages"
-HOMEPAGE="http://gmod.org"
+DESCRIPTION="Display of genomic annotations on interactive web pages"
+HOMEPAGE="http://gmod.org/"
# mirror://sourceforge/gmod/${MY_P}.tar.gz
-# http://search.cpan.org/CPAN/authors/id/L/LD/LDS/GBrowse-2.33.tar.gz
-SRC_URI="http://search.cpan.org/CPAN/authors/id/L/LD/LDS/${MY_P}.tar.gz
- test? ( http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/saccharomyces_cerevisiae.gff.bz2
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/Refseq_Genome_TBLASTX.tar.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/README-gff-files
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/human.gff.tar.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.fasta.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.gff.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.fasta.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.gff.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.fasta.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.gff.gz )"
+# mirror://cpan/authors/id/L/LD/LDS/GBrowse-2.33.tar.gz
+SRC_URI="
+ mirror://cpan/authors/id/L/LD/LDS/${MY_P}.tar.gz
+ test? (
+ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/saccharomyces_cerevisiae.gff.bz2
+ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/Refseq_Genome_TBLASTX.tar.gz
+ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/README-gff-files
+ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/human.gff.tar.gz
+ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.fasta.gz
+ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.gff.gz
+ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.fasta.gz
+ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.gff.gz
+ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.fasta.gz
+ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.gff.gz )"
LICENSE="Artistic"
# webapp ebuilds do not set SLOT
@@ -54,7 +56,6 @@ DEPEND="
# * Bio::DB::Sam is not installed
# * DBD::Pg is not installed
-
RDEPEND="${DEPEND}
>=www-servers/apache-2.0.47
www-apache/mod_fastcgi
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gbrowse/
@ 2011-07-08 14:00 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2011-07-08 14:00 UTC (permalink / raw
To: gentoo-commits
commit: 92c1aa1e11b3bc64bea8df928b8c0c6c0548e4a5
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul 8 13:59:52 2011 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul 8 13:59:52 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=92c1aa1e
sci-biology/gbrowse-2.38: Documented dependency on >=perl-gcpan/Text-ParseWords-3.27, documented requirement of Bio::Root::Version >= 1.0069
(Portage version: 2.1.10.4/git/Linux i686, unsigned Manifest commit)
---
sci-biology/gbrowse/ChangeLog | 5 +++++
sci-biology/gbrowse/gbrowse-2.38.ebuild | 3 +++
2 files changed, 8 insertions(+), 0 deletions(-)
diff --git a/sci-biology/gbrowse/ChangeLog b/sci-biology/gbrowse/ChangeLog
index e36ad47..eaa41a4 100644
--- a/sci-biology/gbrowse/ChangeLog
+++ b/sci-biology/gbrowse/ChangeLog
@@ -2,6 +2,11 @@
# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/generic-genome-browser/ChangeLog,v 1.10 2007/07/29 17:07:38 phreak Exp $
+ 08 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ gbrowse-2.38.ebuild:
+ Added dependency on >=perl-gcpan/Text-ParseWords-3.27, documented requirement
+ of Bio::Root::Version >= 1.0069
+
*gbrowse-2.38 (26 Jun 2011)
26 Jun 2011; Justin Lecher <jlec@gentoo.org> -gbrowse-2.26.ebuild,
diff --git a/sci-biology/gbrowse/gbrowse-2.38.ebuild b/sci-biology/gbrowse/gbrowse-2.38.ebuild
index 9cc3ce4..0d12577 100644
--- a/sci-biology/gbrowse/gbrowse-2.38.ebuild
+++ b/sci-biology/gbrowse/gbrowse-2.38.ebuild
@@ -52,9 +52,12 @@ DEPEND="
# TODO: based on the following message in apache/error_log the list of deps should be longer
# GBROWSE NOTICE: To enable PDF generation, please enter the directory "/home/httpd" and run the commands: "sudo mkdir .inkscape .gnome2" and "sudo chown apache .inkscape .gnome2". To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://127.0.0.1/gbrowse/cgi-bin/gbrowse_details/yeast?ref=chrII;start=90739;end=92028;name=YBL069W;class=Sequence;feature_id=881;db_id=annotations%3Adatabase
+# TODO: implement ebuild checks for these version of packages
+# ! Bio::Root::Version (1.006001) is installed, but we need version >= 1.0069
# * Bio::DB::BigFile is not installed
# * Bio::DB::Sam is not installed
# * DBD::Pg is not installed
+# >=perl-gcpan/Text-ParseWords-3.27
RDEPEND="${DEPEND}
>=www-servers/apache-2.0.47
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gbrowse/
@ 2011-07-08 17:22 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2011-07-08 17:22 UTC (permalink / raw
To: gentoo-commits
commit: 684c1f674268b15688867fee4a4c68689a67b089
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul 8 17:22:27 2011 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul 8 17:22:27 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=684c1f67
sci-biology/gbrowse-2.38: added URL to Bio::DB::Sam
---
sci-biology/gbrowse/gbrowse-2.38.ebuild | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
diff --git a/sci-biology/gbrowse/gbrowse-2.38.ebuild b/sci-biology/gbrowse/gbrowse-2.38.ebuild
index 0d12577..ea981ca 100644
--- a/sci-biology/gbrowse/gbrowse-2.38.ebuild
+++ b/sci-biology/gbrowse/gbrowse-2.38.ebuild
@@ -55,7 +55,7 @@ DEPEND="
# TODO: implement ebuild checks for these version of packages
# ! Bio::Root::Version (1.006001) is installed, but we need version >= 1.0069
# * Bio::DB::BigFile is not installed
-# * Bio::DB::Sam is not installed
+# * Bio::DB::Sam is not installed, install http://cpansearch.perl.org/src/LDS/Bio-SamTools-1.29
# * DBD::Pg is not installed
# >=perl-gcpan/Text-ParseWords-3.27
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gbrowse/
@ 2011-07-30 14:56 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2011-07-30 14:56 UTC (permalink / raw
To: gentoo-commits
commit: ee01dbc0ddcc12b4573686720af26f0f7732b2e4
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Jul 30 14:56:20 2011 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Jul 30 14:56:20 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ee01dbc0
sci-biology/gbrowse: fix typo in an ewarn() message
---
sci-biology/gbrowse/gbrowse-2.39.ebuild | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
diff --git a/sci-biology/gbrowse/gbrowse-2.39.ebuild b/sci-biology/gbrowse/gbrowse-2.39.ebuild
index 0acd25a..35af68f 100644
--- a/sci-biology/gbrowse/gbrowse-2.39.ebuild
+++ b/sci-biology/gbrowse/gbrowse-2.39.ebuild
@@ -144,7 +144,7 @@ src_install() {
pkg_postinst() {
webapp_pkg_postinst || die "webapp_pkg_postinst failed"
- einfo "Please run gbrowse_metadb_config.pl to upate SQlite flatfiles or the live database"
+ einfo "Please run gbrowse_metadb_config.pl to update SQlite flatfiles or the live database"
einfo "This was disabled by "${FILESDIR}"/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm.patch"
}
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gbrowse/
@ 2012-01-17 0:34 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2012-01-17 0:34 UTC (permalink / raw
To: gentoo-commits
commit: f3b9b727f7abb6450e1dd6fbc9bd1d8aeb2ade00
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 17 00:34:09 2012 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 17 00:34:09 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f3b9b727
sci-biology/gbrowse: added dev-perl/TermReadKey to dependencies
(Portage version: 2.1.10.43/git/Linux i686, unsigned Manifest commit)
---
sci-biology/gbrowse/ChangeLog | 6 +++++-
sci-biology/gbrowse/gbrowse-2.39.ebuild | 3 ++-
2 files changed, 7 insertions(+), 2 deletions(-)
diff --git a/sci-biology/gbrowse/ChangeLog b/sci-biology/gbrowse/ChangeLog
index b64e880..c63914a 100644
--- a/sci-biology/gbrowse/ChangeLog
+++ b/sci-biology/gbrowse/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-biology/gbrowse
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/generic-genome-browser/ChangeLog,v 1.10 2007/07/29 17:07:38 phreak Exp $
+ 17 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ gbrowse-2.39.ebuild:
+ added dev-perl/TermReadKey to dependencies
+
30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
gbrowse-2.39.ebuild, +files/disable-gbrowse_metadb_config.pl.patch,
+files/gbrowse_metadb_config.pl.patch, +files/symlink.patch:
diff --git a/sci-biology/gbrowse/gbrowse-2.39.ebuild b/sci-biology/gbrowse/gbrowse-2.39.ebuild
index d4cee63..7f8ab9b 100644
--- a/sci-biology/gbrowse/gbrowse-2.39.ebuild
+++ b/sci-biology/gbrowse/gbrowse-2.39.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
EAPI="2"
@@ -46,6 +46,7 @@ DEPEND="
dev-perl/Statistics-Descriptive
>=dev-perl/Bio-Graphics-1.97
>=dev-perl/JSON-2.510.0
+ dev-perl/TermReadKey
dev-perl/libwww-perl
svg? ( dev-perl/GD-SVG )
pdf? ( media-gfx/inkscape )
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gbrowse/
@ 2012-02-28 16:25 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2012-02-28 16:25 UTC (permalink / raw
To: gentoo-commits
commit: 583d5ee61844e8de863d6133fe83c2fbb00b4bfc
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Feb 28 16:25:27 2012 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Feb 28 16:25:27 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=583d5ee6
sci-biology/gbrowse-2.48: added dependency on <=sci-biology/primer3-2, per http://generic-model-organism-system-database.450254.n5.nabble.com/PrimerDesigner-working-in-2-40-tp4724773p5479669.html
(Portage version: 2.1.10.49/git/Linux x86_64, unsigned Manifest commit)
---
sci-biology/gbrowse/ChangeLog | 8 ++++++++
sci-biology/gbrowse/gbrowse-2.45.ebuild | 2 +-
.../{gbrowse-2.45.ebuild => gbrowse-2.48.ebuild} | 3 ++-
3 files changed, 11 insertions(+), 2 deletions(-)
diff --git a/sci-biology/gbrowse/ChangeLog b/sci-biology/gbrowse/ChangeLog
index 41e2334..b0949c5 100644
--- a/sci-biology/gbrowse/ChangeLog
+++ b/sci-biology/gbrowse/ChangeLog
@@ -2,6 +2,14 @@
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/generic-genome-browser/ChangeLog,v 1.10 2007/07/29 17:07:38 phreak Exp $
+*gbrowse-2.48 (28 Feb 2012)
+
+ 28 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ gbrowse-2.45.ebuild, +gbrowse-2.48.ebuild:
+ added dependency on <=sci-biology/primer3-2, per
+ http://generic-model-organism-system-database.450254.n5.nabble.com/PrimerDesi
+ gner-working-in-2-40-tp4724773p5479669.html
+
*gbrowse-2.45 (17 Jan 2012)
17 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/gbrowse/gbrowse-2.45.ebuild b/sci-biology/gbrowse/gbrowse-2.45.ebuild
index f914844..4b3f3b3 100644
--- a/sci-biology/gbrowse/gbrowse-2.45.ebuild
+++ b/sci-biology/gbrowse/gbrowse-2.45.ebuild
@@ -44,7 +44,7 @@ DEPEND="!!sci-biology/GBrowse
virtual/perl-Digest-MD5
>=dev-perl/CGI-Session-4.03
dev-perl/Statistics-Descriptive
- >=dev-perl/Bio-Graphics-1.97
+ >=dev-perl/Bio-Graphics-2.26
>=dev-perl/JSON-2.510.0
dev-perl/TermReadKey
dev-perl/libwww-perl
diff --git a/sci-biology/gbrowse/gbrowse-2.45.ebuild b/sci-biology/gbrowse/gbrowse-2.48.ebuild
similarity index 99%
copy from sci-biology/gbrowse/gbrowse-2.45.ebuild
copy to sci-biology/gbrowse/gbrowse-2.48.ebuild
index f914844..754cc9e 100644
--- a/sci-biology/gbrowse/gbrowse-2.45.ebuild
+++ b/sci-biology/gbrowse/gbrowse-2.48.ebuild
@@ -44,7 +44,7 @@ DEPEND="!!sci-biology/GBrowse
virtual/perl-Digest-MD5
>=dev-perl/CGI-Session-4.03
dev-perl/Statistics-Descriptive
- >=dev-perl/Bio-Graphics-1.97
+ >=dev-perl/Bio-Graphics-2.26
>=dev-perl/JSON-2.510.0
dev-perl/TermReadKey
dev-perl/libwww-perl
@@ -86,6 +86,7 @@ RDEPEND="${DEPEND}
postgres? ( >=dev-perl/Bio-DB-Das-Chado-0.32 )
>=dev-perl/Bio-SamTools-1.29
>=dev-perl/Bio-BigFile-1.06
+ <=sci-biology/primer3-2
)"
src_prepare() {
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gbrowse/
@ 2012-05-22 19:43 Justin Lecher
0 siblings, 0 replies; 9+ messages in thread
From: Justin Lecher @ 2012-05-22 19:43 UTC (permalink / raw
To: gentoo-commits
commit: 543741f7d916e0d1ed000aff489675e34bc96c32
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue May 22 19:07:50 2012 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue May 22 19:07:50 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=543741f7
sci-biology/gbrowse: Add missing eutils.eclass, bump to EAPI=4, remove unnecessary bits
(Portage version: 2.2.0_alpha107/git/Linux x86_64, RepoMan options: --force, unsigned Manifest commit)
---
sci-biology/gbrowse/ChangeLog | 4 ++++
sci-biology/gbrowse/gbrowse-2.39.ebuild | 20 +++++++++++---------
sci-biology/gbrowse/gbrowse-2.45.ebuild | 18 ++++++++++--------
sci-biology/gbrowse/gbrowse-2.48.ebuild | 18 ++++++++++--------
4 files changed, 35 insertions(+), 25 deletions(-)
diff --git a/sci-biology/gbrowse/ChangeLog b/sci-biology/gbrowse/ChangeLog
index b0949c5..9343242 100644
--- a/sci-biology/gbrowse/ChangeLog
+++ b/sci-biology/gbrowse/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/generic-genome-browser/ChangeLog,v 1.10 2007/07/29 17:07:38 phreak Exp $
+ 22 May 2012; Justin Lecher <jlec@gentoo.org> gbrowse-2.39.ebuild,
+ gbrowse-2.45.ebuild, gbrowse-2.48.ebuild:
+ Add missing eutils.eclass, bump to EAPI=4, remove unnecessary bits
+
*gbrowse-2.48 (28 Feb 2012)
28 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/gbrowse/gbrowse-2.39.ebuild b/sci-biology/gbrowse/gbrowse-2.39.ebuild
index 7f8ab9b..47d02f9 100644
--- a/sci-biology/gbrowse/gbrowse-2.39.ebuild
+++ b/sci-biology/gbrowse/gbrowse-2.39.ebuild
@@ -1,9 +1,10 @@
# Copyright 1999-2012 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI="2"
-inherit perl-module webapp
+EAPI=4
+
+inherit eutils perl-module webapp
MY_P="GBrowse-${PV}"
@@ -91,12 +92,13 @@ RDEPEND="${DEPEND}
src_prepare() {
sed -i 's/return unless -t STDIN/return/' install_util/GBrowseInstall.pm || die
sed -i 's/process_/bp_process_/g' INSTALL || die
- epatch "${FILESDIR}"/GBrowseInstall.pm-"${PV}".patch || die "Failed to apply GBrowseInstall.pm-"${PV}".patch"
- epatch "${FILESDIR}"/destdir.patch || die "Failed to apply destdir.patch"
- epatch "${FILESDIR}"/fix-PNG-export.patch || die "Failed to apply fix-PNG-export.patch"
- epatch "${FILESDIR}"/symlink.patch || die "Failed to apply symlink.patch"
- epatch "${FILESDIR}"/gbrowse_metadb_config.pl.patch || die "Failed to apply gbrowse_metadb_config.pl.patch"
- epatch "${FILESDIR}"/disable-gbrowse_metadb_config.pl.patch || die "Failed to apply disable-gbrowse_metadb_config.pl.patch"
+ epatch \
+ "${FILESDIR}"/GBrowseInstall.pm-"${PV}".patch \
+ "${FILESDIR}"/destdir.patch \
+ "${FILESDIR}"/fix-PNG-export.patch \
+ "${FILESDIR}"/symlink.patch \
+ "${FILESDIR}"/gbrowse_metadb_config.pl.patch \
+ "${FILESDIR}"/disable-gbrowse_metadb_config.pl.patch
}
src_configure() {
@@ -143,7 +145,7 @@ src_install() {
einfo "Make sure you compiled apache with +cgi and copy ${FILESDIR}/gbrowse.conf.vhosts.d to /etc/apache2/vhosts.d/"
sed -i "s#"${D}"##g" "${S}"/install_util/GBrowseInstall.pm || die
- sed -i "s#"${D}"##" "${S}"/blib/conf/GBrowse.conf*
+ sed -i "s#"${D}"##" "${S}"/blib/conf/GBrowse.conf* || die
sed -i 's#DBI:SQLite:'${D}'/var/www/gbrowse2/databases/#DBI:SQLite:/var/www/gbrowse2/databases/#' "${S}"/install_util/GBrowseInstall.pm || die
}
diff --git a/sci-biology/gbrowse/gbrowse-2.45.ebuild b/sci-biology/gbrowse/gbrowse-2.45.ebuild
index 4b3f3b3..f1b510f 100644
--- a/sci-biology/gbrowse/gbrowse-2.45.ebuild
+++ b/sci-biology/gbrowse/gbrowse-2.45.ebuild
@@ -1,9 +1,10 @@
# Copyright 1999-2012 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI="2"
-inherit perl-module webapp
+EAPI=4
+
+inherit eutils perl-module webapp
MY_P="GBrowse-${PV}"
@@ -91,12 +92,13 @@ RDEPEND="${DEPEND}
src_prepare() {
sed -i 's/return unless -t STDIN/return/' install_util/GBrowseInstall.pm || die "Failed to kill the interactive behavior of install_util/GBrowseInstall.pm"
sed -i 's/process_/bp_process_/g' INSTALL || die "Failed to prepend bp_ prefix to INSTALL file"
- epatch "${FILESDIR}"/GBrowseInstall.pm-"${PV}".patch || die "Failed to apply GBrowseInstall.pm-"${PV}".patch"
- epatch "${FILESDIR}"/destdir.patch || die "Failed to apply destdir.patch"
- epatch "${FILESDIR}"/fix-PNG-export.patch || die "Failed to apply fix-PNG-export.patch"
- epatch "${FILESDIR}"/symlink.patch || die "Failed to apply symlink.patch"
- epatch "${FILESDIR}"/gbrowse_metadb_config.pl.patch || die "Failed to apply gbrowse_metadb_config.pl.patch"
- epatch "${FILESDIR}"/disable-gbrowse_metadb_config.pl.patch || die "Failed to apply disable-gbrowse_metadb_config.pl.patch"
+ epatch \
+ "${FILESDIR}"/GBrowseInstall.pm-"${PV}".patch \
+ "${FILESDIR}"/destdir.patch \
+ "${FILESDIR}"/fix-PNG-export.patch \
+ "${FILESDIR}"/symlink.patch \
+ "${FILESDIR}"/gbrowse_metadb_config.pl.patch \
+ "${FILESDIR}"/disable-gbrowse_metadb_config.pl.patch
for f in conf/synteny/wild_rice_synteny.conf conf/synteny/rice_synteny.conf conf/GBrowse.conf \
htdocs/tutorial/tutorial.html htdocs/index.html lib/Bio/Graphics/Browser2/Action.pm \
Changes; do
diff --git a/sci-biology/gbrowse/gbrowse-2.48.ebuild b/sci-biology/gbrowse/gbrowse-2.48.ebuild
index 754cc9e..20987d9 100644
--- a/sci-biology/gbrowse/gbrowse-2.48.ebuild
+++ b/sci-biology/gbrowse/gbrowse-2.48.ebuild
@@ -1,9 +1,10 @@
# Copyright 1999-2012 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI="2"
-inherit perl-module webapp
+EAPI=4
+
+inherit eutils perl-module webapp
MY_P="GBrowse-${PV}"
@@ -92,12 +93,13 @@ RDEPEND="${DEPEND}
src_prepare() {
sed -i 's/return unless -t STDIN/return/' install_util/GBrowseInstall.pm || die "Failed to kill the interactive behavior of install_util/GBrowseInstall.pm"
sed -i 's/process_/bp_process_/g' INSTALL || die "Failed to prepend bp_ prefix to INSTALL file"
- epatch "${FILESDIR}"/GBrowseInstall.pm-"${PV}".patch || die "Failed to apply GBrowseInstall.pm-"${PV}".patch"
- epatch "${FILESDIR}"/destdir.patch || die "Failed to apply destdir.patch"
- epatch "${FILESDIR}"/fix-PNG-export.patch || die "Failed to apply fix-PNG-export.patch"
- epatch "${FILESDIR}"/symlink.patch || die "Failed to apply symlink.patch"
- epatch "${FILESDIR}"/gbrowse_metadb_config.pl.patch || die "Failed to apply gbrowse_metadb_config.pl.patch"
- epatch "${FILESDIR}"/disable-gbrowse_metadb_config.pl.patch || die "Failed to apply disable-gbrowse_metadb_config.pl.patch"
+ epatch \
+ "${FILESDIR}"/GBrowseInstall.pm-"${PV}".patch \
+ "${FILESDIR}"/destdir.patch \
+ "${FILESDIR}"/fix-PNG-export.patch \
+ "${FILESDIR}"/symlink.patch \
+ "${FILESDIR}"/gbrowse_metadb_config.pl.patch \
+ "${FILESDIR}"/disable-gbrowse_metadb_config.pl.patch
for f in conf/synteny/wild_rice_synteny.conf conf/synteny/rice_synteny.conf conf/GBrowse.conf \
htdocs/tutorial/tutorial.html htdocs/index.html lib/Bio/Graphics/Browser2/Action.pm \
Changes; do
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gbrowse/
@ 2014-09-24 6:45 Justin Lecher
0 siblings, 0 replies; 9+ messages in thread
From: Justin Lecher @ 2014-09-24 6:45 UTC (permalink / raw
To: gentoo-commits
commit: 66cf9e669374c000ca06c72939549e9231326ad5
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Sep 24 06:35:02 2014 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Sep 24 06:35:02 2014 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=66cf9e66
sci-biology/gbrowse: Bump to EAPI=5
Package-Manager: portage-2.2.13
---
sci-biology/gbrowse/ChangeLog | 6 +++++-
sci-biology/gbrowse/gbrowse-2.39.ebuild | 4 ++--
sci-biology/gbrowse/gbrowse-2.45.ebuild | 4 ++--
sci-biology/gbrowse/gbrowse-2.48.ebuild | 4 ++--
sci-biology/gbrowse/metadata.xml | 14 +++++++-------
5 files changed, 18 insertions(+), 14 deletions(-)
diff --git a/sci-biology/gbrowse/ChangeLog b/sci-biology/gbrowse/ChangeLog
index 9343242..701feba 100644
--- a/sci-biology/gbrowse/ChangeLog
+++ b/sci-biology/gbrowse/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-biology/gbrowse
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/generic-genome-browser/ChangeLog,v 1.10 2007/07/29 17:07:38 phreak Exp $
+ 24 Sep 2014; Justin Lecher <jlec@gentoo.org> gbrowse-2.39.ebuild,
+ gbrowse-2.45.ebuild, gbrowse-2.48.ebuild, metadata.xml:
+ Bump to EAPI=5
+
22 May 2012; Justin Lecher <jlec@gentoo.org> gbrowse-2.39.ebuild,
gbrowse-2.45.ebuild, gbrowse-2.48.ebuild:
Add missing eutils.eclass, bump to EAPI=4, remove unnecessary bits
diff --git a/sci-biology/gbrowse/gbrowse-2.39.ebuild b/sci-biology/gbrowse/gbrowse-2.39.ebuild
index f344218..0edfba5 100644
--- a/sci-biology/gbrowse/gbrowse-2.39.ebuild
+++ b/sci-biology/gbrowse/gbrowse-2.39.ebuild
@@ -2,7 +2,7 @@
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=4
+EAPI=5
inherit eutils perl-module webapp
@@ -37,7 +37,7 @@ S="${WORKDIR}/${MY_P}"
# how about mod_fcgi and dev-libs/fcgi and mod_scgi?
DEPEND="
>=perl-core/Module-Build-0.380.0
- >=dev-lang/perl-5.8.8
+ >=dev-lang/perl-5.8.8:=
dev-perl/Capture-Tiny
>=sci-biology/bioperl-1.6.901
>=dev-perl/GD-2.07
diff --git a/sci-biology/gbrowse/gbrowse-2.45.ebuild b/sci-biology/gbrowse/gbrowse-2.45.ebuild
index c42922d..e0ab203 100644
--- a/sci-biology/gbrowse/gbrowse-2.45.ebuild
+++ b/sci-biology/gbrowse/gbrowse-2.45.ebuild
@@ -2,7 +2,7 @@
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=4
+EAPI=5
inherit eutils perl-module webapp
@@ -37,7 +37,7 @@ S="${WORKDIR}/${MY_P}"
# how about mod_fcgi and dev-libs/fcgi and mod_scgi?
DEPEND="!!sci-biology/GBrowse
>=perl-core/Module-Build-0.380.0
- >=dev-lang/perl-5.8.8
+ >=dev-lang/perl-5.8.8:=
dev-perl/Capture-Tiny
>=sci-biology/bioperl-1.6.901
>=dev-perl/GD-2.07
diff --git a/sci-biology/gbrowse/gbrowse-2.48.ebuild b/sci-biology/gbrowse/gbrowse-2.48.ebuild
index b844e94..b61cdd3 100644
--- a/sci-biology/gbrowse/gbrowse-2.48.ebuild
+++ b/sci-biology/gbrowse/gbrowse-2.48.ebuild
@@ -2,7 +2,7 @@
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=4
+EAPI=5
inherit eutils perl-module webapp
@@ -37,7 +37,7 @@ S="${WORKDIR}/${MY_P}"
# how about mod_fcgi and dev-libs/fcgi and mod_scgi?
DEPEND="!!sci-biology/GBrowse
>=perl-core/Module-Build-0.380.0
- >=dev-lang/perl-5.8.8
+ >=dev-lang/perl-5.8.8:=
dev-perl/Capture-Tiny
>=sci-biology/bioperl-1.6.901
>=dev-perl/GD-2.07
diff --git a/sci-biology/gbrowse/metadata.xml b/sci-biology/gbrowse/metadata.xml
index 2618ccd..61916cb 100644
--- a/sci-biology/gbrowse/metadata.xml
+++ b/sci-biology/gbrowse/metadata.xml
@@ -1,13 +1,13 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer>
- <email>weaver@gentoo.org</email>
- <name>Andrey Kislyuk</name>
- <description>GBrowse is a generic genome browser.</description>
- </maintainer>
- <herd>sci-biology</herd>
- <longdescription lang="en">
+ <maintainer>
+ <email>weaver@gentoo.org</email>
+ <name>Andrey Kislyuk</name>
+ <description>GBrowse is a generic genome browser.</description>
+ </maintainer>
+ <herd>sci-biology</herd>
+ <longdescription lang="en">
GBrowse is a generic genome browser written in perl, could run as CGI, under mod_perl. Something called Apache::Registry should make it faster. It uses mysql or postgres as the storage engine.
</longdescription>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gbrowse/
@ 2014-11-13 13:00 Justin Lecher
0 siblings, 0 replies; 9+ messages in thread
From: Justin Lecher @ 2014-11-13 13:00 UTC (permalink / raw
To: gentoo-commits
commit: 01335d59fc612ee994449e1531943e61c1a2309c
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Nov 13 12:47:40 2014 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Nov 13 12:47:40 2014 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=01335d59
sci-biology/gbrowse: Use perl virtuals instead of core
Package-Manager: portage-2.2.14
---
sci-biology/gbrowse/ChangeLog | 4 ++++
sci-biology/gbrowse/gbrowse-2.39.ebuild | 6 +++---
sci-biology/gbrowse/gbrowse-2.45.ebuild | 6 +++---
sci-biology/gbrowse/gbrowse-2.48.ebuild | 6 +++---
4 files changed, 13 insertions(+), 9 deletions(-)
diff --git a/sci-biology/gbrowse/ChangeLog b/sci-biology/gbrowse/ChangeLog
index 701feba..c67d2a1 100644
--- a/sci-biology/gbrowse/ChangeLog
+++ b/sci-biology/gbrowse/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/generic-genome-browser/ChangeLog,v 1.10 2007/07/29 17:07:38 phreak Exp $
+ 13 Nov 2014; Justin Lecher <jlec@gentoo.org> gbrowse-2.39.ebuild,
+ gbrowse-2.45.ebuild, gbrowse-2.48.ebuild:
+ Use perl virtuals instead of core
+
24 Sep 2014; Justin Lecher <jlec@gentoo.org> gbrowse-2.39.ebuild,
gbrowse-2.45.ebuild, gbrowse-2.48.ebuild, metadata.xml:
Bump to EAPI=5
diff --git a/sci-biology/gbrowse/gbrowse-2.39.ebuild b/sci-biology/gbrowse/gbrowse-2.39.ebuild
index 0edfba5..6d86c72 100644
--- a/sci-biology/gbrowse/gbrowse-2.39.ebuild
+++ b/sci-biology/gbrowse/gbrowse-2.39.ebuild
@@ -36,7 +36,7 @@ S="${WORKDIR}/${MY_P}"
# TODO: dev-perl/MOBY, dev-perl/Bio-SCF, dev-perl/Safe-World (not compatible w/perl-5.10)
# how about mod_fcgi and dev-libs/fcgi and mod_scgi?
DEPEND="
- >=perl-core/Module-Build-0.380.0
+ >=virtual/perl-Module-Build-0.380.0
>=dev-lang/perl-5.8.8:=
dev-perl/Capture-Tiny
>=sci-biology/bioperl-1.6.901
@@ -67,8 +67,8 @@ RDEPEND="${DEPEND}
!minimal? (
dev-perl/File-NFSLock
dev-perl/FCGI
- perl-core/Math-BigInt
- perl-core/Math-BigInt-FastCalc
+ virtual/perl-Math-BigInt
+ virtual/perl-Math-BigInt-FastCalc
dev-perl/Math-BigInt-GMP
dev-perl/Digest-SHA1
dev-perl/Crypt-SSLeay
diff --git a/sci-biology/gbrowse/gbrowse-2.45.ebuild b/sci-biology/gbrowse/gbrowse-2.45.ebuild
index e0ab203..c853723 100644
--- a/sci-biology/gbrowse/gbrowse-2.45.ebuild
+++ b/sci-biology/gbrowse/gbrowse-2.45.ebuild
@@ -36,7 +36,7 @@ S="${WORKDIR}/${MY_P}"
# TODO: dev-perl/MOBY, dev-perl/Bio-SCF, dev-perl/Safe-World (not compatible w/perl-5.10)
# how about mod_fcgi and dev-libs/fcgi and mod_scgi?
DEPEND="!!sci-biology/GBrowse
- >=perl-core/Module-Build-0.380.0
+ >=virtual/perl-Module-Build-0.380.0
>=dev-lang/perl-5.8.8:=
dev-perl/Capture-Tiny
>=sci-biology/bioperl-1.6.901
@@ -67,8 +67,8 @@ RDEPEND="${DEPEND}
!minimal? (
dev-perl/File-NFSLock
dev-perl/FCGI
- perl-core/Math-BigInt
- perl-core/Math-BigInt-FastCalc
+ virtual/perl-Math-BigInt
+ virtual/perl-Math-BigInt-FastCalc
dev-perl/Math-BigInt-GMP
dev-perl/Digest-SHA1
dev-perl/Crypt-SSLeay
diff --git a/sci-biology/gbrowse/gbrowse-2.48.ebuild b/sci-biology/gbrowse/gbrowse-2.48.ebuild
index b61cdd3..427462c 100644
--- a/sci-biology/gbrowse/gbrowse-2.48.ebuild
+++ b/sci-biology/gbrowse/gbrowse-2.48.ebuild
@@ -36,7 +36,7 @@ S="${WORKDIR}/${MY_P}"
# TODO: dev-perl/MOBY, dev-perl/Bio-SCF, dev-perl/Safe-World (not compatible w/perl-5.10)
# how about mod_fcgi and dev-libs/fcgi and mod_scgi?
DEPEND="!!sci-biology/GBrowse
- >=perl-core/Module-Build-0.380.0
+ >=virtual/perl-Module-Build-0.380.0
>=dev-lang/perl-5.8.8:=
dev-perl/Capture-Tiny
>=sci-biology/bioperl-1.6.901
@@ -67,8 +67,8 @@ RDEPEND="${DEPEND}
!minimal? (
dev-perl/File-NFSLock
dev-perl/FCGI
- perl-core/Math-BigInt
- perl-core/Math-BigInt-FastCalc
+ virtual/perl-Math-BigInt
+ virtual/perl-Math-BigInt-FastCalc
dev-perl/Math-BigInt-GMP
dev-perl/Digest-SHA1
dev-perl/Crypt-SSLeay
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2014-09-24 6:45 [gentoo-commits] proj/sci:master commit in: sci-biology/gbrowse/ Justin Lecher
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2012-05-22 19:43 Justin Lecher
2012-02-28 16:25 Martin Mokrejs
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2011-07-30 14:56 Martin Mokrejs
2011-07-08 17:22 Martin Mokrejs
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2011-06-25 17:22 Justin Lecher
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