From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from ) id 1QaWe8-00039w-US for garchives@archives.gentoo.org; Sat, 25 Jun 2011 17:27:53 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 534FA1C1AD; Sat, 25 Jun 2011 17:22:04 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id EF9E21C17F for ; Sat, 25 Jun 2011 17:22:03 +0000 (UTC) Received: from pelican.gentoo.org (unknown [66.219.59.40]) (using TLSv1 with cipher ADH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 45A5E2AC088 for ; Sat, 25 Jun 2011 17:22:03 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by pelican.gentoo.org (Postfix) with ESMTP id 6509480504 for ; Sat, 25 Jun 2011 17:22:02 +0000 (UTC) From: "Justin Lecher" To: gentoo-commits@lists.gentoo.org Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Justin Lecher" Message-ID: Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/gbrowse/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/gbrowse/ChangeLog sci-biology/gbrowse/gbrowse-1.70.ebuild sci-biology/gbrowse/gbrowse-2.00.ebuild sci-biology/gbrowse/gbrowse-2.26.ebuild sci-biology/gbrowse/gbrowse-2.33.ebuild X-VCS-Directories: sci-biology/gbrowse/ X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: c051a8f8d54dd27ef4247923cc4fec182b6548df Date: Sat, 25 Jun 2011 17:22:02 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: quoted-printable X-Archives-Salt: X-Archives-Hash: a83243d89dc3bf86e11393a8e904d433 commit: c051a8f8d54dd27ef4247923cc4fec182b6548df Author: Justin Lecher gentoo org> AuthorDate: Sat Jun 25 14:29:32 2011 +0000 Commit: Justin Lecher gentoo org> CommitDate: Sat Jun 25 14:29:32 2011 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=3Dproj/sci.git;a=3Dc= ommit;h=3Dc051a8f8 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/ChangeLo= g 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/Ch= angeLog,v 1.10 2007/07/29 17:07:38 phreak Exp $ =20 + 25 Jun 2011; Justin Lecher -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 thirdpartymirro= rs + 05 Feb 2010; Andrey Kislyuk ChangeLog: Version bump =20 diff --git a/sci-biology/gbrowse/gbrowse-1.70.ebuild b/sci-biology/gbrows= e/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/ge= neric-genome-browser-1.58.ebuild,v 1.9 2007/07/29 17:07:38 phreak Exp $ - -EAPI=3D"2" - -inherit perl-module webapp - -MY_P=3D"Generic-Genome-Browser-${PV}" - -DESCRIPTION=3D"The generic genome browser provides a display of genomic = annotations on interactive web pages" -HOMEPAGE=3D"http://gmod.org" -SRC_URI=3D"mirror://sourceforge/gmod/${MY_P}.tar.gz" - -LICENSE=3D"Artistic" -# webapp ebuilds do not set SLOT -KEYWORDS=3D"~x86 ~amd64" -IUSE=3D"-minimal" # lwp moby scf - -S=3D"${WORKDIR}/${MY_P}" - -# TODO: dev-perl/MOBY, dev-perl/Bio-SCF, dev-perl/libwww-perl, LWP -DEPEND=3D">=3Ddev-lang/perl-5.8.8 - >=3Dsci-biology/bioperl-1.6 - >=3Ddev-perl/GD-2.07 - dev-perl/IO-String - virtual/perl-Digest-MD5 - >=3Ddev-perl/CGI-Session-4.03 - dev-perl/Statistics-Descriptive - >=3Ddev-perl/Bio-Graphics-1.97" -RDEPEND=3D"${DEPEND} - >=3Dwww-servers/apache-2.0.47 - >=3Dvirtual/perl-CGI-2.56 - dev-perl/DBI - dev-perl/DBD-mysql - dev-perl/Class-Base - dev-perl/Text-Shellwords - !minimal? ( - dev-perl/XML-Parser - dev-perl/XML-Writer - dev-perl/XML-Twig - dev-perl/XML-DOM - dev-perl/GD-SVG - dev-perl/Bio-Das - )" - -src_configure() { - webapp_src_preinst - perl Makefile.PL \ - HTDOCS=3D"${D}/${MY_HTDOCSDIR}" \ - CGIBIN=3D"${D}/${MY_HTDOCSDIR}/cgi-bin" \ - CONF=3D"${D}/etc" \ - PREFIX=3D"${D}/usr" \ - PACKAGE_DIR=3D"${D}" \ - INSTALLDIRS=3Dvendor \ - GBROWSE_ROOT=3Dgbrowse \ - DESTDIR=3D"${ROOT}" \ - || die -} - -src_install() { - mydoc=3D"Changes README TODO INSTALL" - perl-module_src_install - - # TODO: write our own readme - webapp_postinst_txt en "${S}/INSTALL" - webapp_src_install -} diff --git a/sci-biology/gbrowse/gbrowse-2.00.ebuild b/sci-biology/gbrows= e/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/ge= neric-genome-browser-1.58.ebuild,v 1.9 2007/07/29 17:07:38 phreak Exp $ - -EAPI=3D"2" - -inherit perl-module webapp - -MY_P=3D"GBrowse-${PV}" - -DESCRIPTION=3D"The generic genome browser provides a display of genomic = annotations on interactive web pages" -HOMEPAGE=3D"http://gmod.org" -SRC_URI=3D"mirror://sourceforge/gmod/${MY_P}.tar.gz" - -LICENSE=3D"Artistic" -# webapp ebuilds do not set SLOT -KEYWORDS=3D"~x86 ~amd64" -IUSE=3D"-minimal" # lwp moby scf - -S=3D"${WORKDIR}/${MY_P}" - -# TODO: dev-perl/MOBY, dev-perl/Bio-SCF, dev-perl/Safe-World (not compat= ible w/perl-5.10) -DEPEND=3D">=3Ddev-lang/perl-5.8.8 - >=3Dsci-biology/bioperl-1.6 - >=3Ddev-perl/GD-2.07 - dev-perl/IO-String - virtual/perl-Digest-MD5 - >=3Ddev-perl/CGI-Session-4.03 - dev-perl/Statistics-Descriptive - >=3Ddev-perl/Bio-Graphics-1.97 - dev-perl/JSON - dev-perl/libwww-perl" -RDEPEND=3D"${DEPEND} - >=3Dwww-servers/apache-2.0.47 - dev-perl/DBI - || ( dev-perl/DBD-Pg dev-perl/DBD-mysql ) - !minimal? ( - dev-perl/File-NFSLock - dev-perl/FCGI - perl-core/Math-BigInt - dev-perl/Digest-SHA1 - dev-perl/Crypt-SSLeay - dev-perl/Net-SMTP-SSL - dev-perl/GD-SVG - dev-perl/Net-OpenID-Consumer - virtual/perl-DB_File - dev-perl/DB_File-Lock - )" - -src_prepare() { - sed -i 's/return unless -t STDIN/return/' install_util/GBrowseInstall.p= m || die -} - -src_configure() { - webapp_src_preinst - perl Makefile.PL \ - HTDOCS=3D"${D}/${MY_HTDOCSDIR}" \ - CGIBIN=3D"${D}/${MY_HTDOCSDIR}/cgi-bin" \ - CONF=3D"${D}/etc" \ - PREFIX=3D"${D}/usr" \ - PACKAGE_DIR=3D"${D}" \ - INSTALLDIRS=3Dvendor \ - GBROWSE_ROOT=3Dgbrowse \ - DESTDIR=3D"${ROOT}" \ - || die -} - -src_install() { - mydoc=3D"Changes README TODO INSTALL" - perl-module_src_install - - # TODO: write our own readme - webapp_postinst_txt en "${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/gbrows= e/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=3D"2" @@ -7,19 +7,21 @@ inherit perl-module webapp =20 MY_P=3D"GBrowse-${PV}" =20 -DESCRIPTION=3D"The generic genome browser provides a display of genomic = annotations on interactive web pages" -HOMEPAGE=3D"http://gmod.org" -SRC_URI=3D"mirror://sourceforge/gmod/${MY_P}.tar.gz - test? ( http://sourceforge.net/projects/gmod/files/Generic%20Genome%20B= rowser/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=3D"Display of genomic annotations on interactive web pages" +HOMEPAGE=3D"http://gmod.org/" +SRC_URI=3D" + mirror://sourceforge/gmod/${MY_P}.tar.gz + test? ( + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/= Sample%20Data%20Files/saccharomyces_cerevisiae.gff.bz2 + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/= Sample%20Data%20Files/Refseq_Genome_TBLASTX.tar.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/= Sample%20Data%20Files/README-gff-files + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/= Sample%20Data%20Files/human.gff.tar.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/= Sample%20Data%20Files/yeast.fasta.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/= Sample%20Data%20Files/yeast.gff.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/= Sample%20Data%20Files/worm.fasta.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/= Sample%20Data%20Files/worm.gff.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/= Sample%20Data%20Files/fly.fasta.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/= Sample%20Data%20Files/fly.gff.gz )" =20 LICENSE=3D"Artistic" # webapp ebuilds do not set SLOT @@ -30,7 +32,8 @@ S=3D"${WORKDIR}/${MY_P}" =20 # TODO: dev-perl/MOBY, dev-perl/Bio-SCF, dev-perl/Safe-World (not compat= ible w/perl-5.10) # TODO: make sure www-servers/apache +cgi -DEPEND=3D">=3Ddev-lang/perl-5.8.8 +DEPEND=3D" + >=3Ddev-lang/perl-5.8.8 dev-perl/Capture-Tiny >=3Dsci-biology/bioperl-1.6 >=3Ddev-perl/GD-2.07 diff --git a/sci-biology/gbrowse/gbrowse-2.33.ebuild b/sci-biology/gbrows= e/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=3D"2" @@ -7,21 +7,23 @@ inherit perl-module webapp =20 MY_P=3D"GBrowse-${PV}" =20 -DESCRIPTION=3D"The generic genome browser provides a display of genomic = annotations on interactive web pages" -HOMEPAGE=3D"http://gmod.org" +DESCRIPTION=3D"Display of genomic annotations on interactive web pages" +HOMEPAGE=3D"http://gmod.org/" # mirror://sourceforge/gmod/${MY_P}.tar.gz -# http://search.cpan.org/CPAN/authors/id/L/LD/LDS/GBrowse-2.33.tar.gz -SRC_URI=3D"http://search.cpan.org/CPAN/authors/id/L/LD/LDS/${MY_P}.tar.g= z - test? ( http://sourceforge.net/projects/gmod/files/Generic%20Genome%20B= rowser/Sample%20Data%20Files/saccharomyces_cerevisiae.gff.bz2 - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser= /Sample%20Data%20Files/Refseq_Genome_TBLASTX.tar.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser= /Sample%20Data%20Files/README-gff-files - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser= /Sample%20Data%20Files/human.gff.tar.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser= /Sample%20Data%20Files/yeast.fasta.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser= /Sample%20Data%20Files/yeast.gff.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser= /Sample%20Data%20Files/worm.fasta.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser= /Sample%20Data%20Files/worm.gff.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser= /Sample%20Data%20Files/fly.fasta.gz - http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser= /Sample%20Data%20Files/fly.gff.gz )" +# mirror://cpan/authors/id/L/LD/LDS/GBrowse-2.33.tar.gz +SRC_URI=3D" + mirror://cpan/authors/id/L/LD/LDS/${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 )" =20 LICENSE=3D"Artistic" # webapp ebuilds do not set SLOT @@ -54,7 +56,6 @@ DEPEND=3D" # * Bio::DB::Sam is not installed # * DBD::Pg is not installed =20 - RDEPEND=3D"${DEPEND} >=3Dwww-servers/apache-2.0.47 www-apache/mod_fastcgi