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From: "Justin Lecher" <jlec@gentoo.org>
To: gentoo-commits@lists.gentoo.org
Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/gbrowse/
Date: Sat, 25 Jun 2011 17:22:02 +0000 (UTC)	[thread overview]
Message-ID: <c051a8f8d54dd27ef4247923cc4fec182b6548df.jlec@gentoo> (raw)

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



             reply	other threads:[~2011-06-25 17:27 UTC|newest]

Thread overview: 9+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2011-06-25 17:22 Justin Lecher [this message]
  -- strict thread matches above, loose matches on Subject: below --
2011-07-08 14:00 [gentoo-commits] proj/sci:master commit in: sci-biology/gbrowse/ Martin Mokrejs
2011-07-08 17:22 Martin Mokrejs
2011-07-30 14:56 Martin Mokrejs
2012-01-17  0:34 Martin Mokrejs
2012-02-28 16:25 Martin Mokrejs
2012-05-22 19:43 Justin Lecher
2014-09-24  6:45 Justin Lecher
2014-11-13 13:00 Justin Lecher

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