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 1Qbbwd-0001K7-AF for garchives@archives.gentoo.org; Tue, 28 Jun 2011 17:19:27 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 5466B1C05F; Tue, 28 Jun 2011 17:15:11 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id 9A9DF1C05F for ; Tue, 28 Jun 2011 17:15:10 +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 42C511BC022 for ; Tue, 28 Jun 2011 17:15:08 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by pelican.gentoo.org (Postfix) with ESMTP id 7BCDC8003C for ; Tue, 28 Jun 2011 17:15:07 +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/files/, sci-biology/gbrowse/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/gbrowse/ChangeLog sci-biology/gbrowse/files/GBrowseInstall.pm-2.26.patch sci-biology/gbrowse/files/GBrowseInstall.pm-2.33.patch sci-biology/gbrowse/files/GBrowseInstall.pm-2.38.patch sci-biology/gbrowse/files/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm-2.26.patch sci-biology/gbrowse/gbrowse-2.26.ebuild sci-biology/gbrowse/gbrowse-2.33.ebuild sci-biology/gbrowse/gbrowse-2.38.ebuild X-VCS-Directories: sci-biology/gbrowse/files/ sci-biology/gbrowse/ X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: a50c105c259094c0b358fb024a326dccc3751247 Date: Tue, 28 Jun 2011 17:15:07 +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: 5497c87ae17d59e7d48ac2fb562c459e commit: a50c105c259094c0b358fb024a326dccc3751247 Author: Justin Lecher gentoo org> AuthorDate: Sun Jun 26 08:02:44 2011 +0000 Commit: Justin Lecher gentoo org> CommitDate: Sun Jun 26 08:02:44 2011 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=3Dproj/sci.git;a=3Dc= ommit;h=3Da50c105c Version Bump (Portage version: 2.2.0_alpha41/git/Linux x86_64, signed Manifest commit = with key 70EB7916) --- sci-biology/gbrowse/ChangeLog | 9 + .../gbrowse/files/GBrowseInstall.pm-2.26.patch | 72 -------- ....pm-2.33.patch =3D> GBrowseInstall.pm-2.38.patch} | 0 ...-disable-gbrowse_metadb_config.pl.pm-2.26.patch | 21 --- sci-biology/gbrowse/gbrowse-2.26.ebuild | 170 --------------= ------ .../{gbrowse-2.33.ebuild =3D> gbrowse-2.38.ebuild} | 0 6 files changed, 9 insertions(+), 263 deletions(-) diff --git a/sci-biology/gbrowse/ChangeLog b/sci-biology/gbrowse/ChangeLo= g index b66d69a..e36ad47 100644 --- a/sci-biology/gbrowse/ChangeLog +++ b/sci-biology/gbrowse/ChangeLog @@ -2,6 +2,15 @@ # 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 +*gbrowse-2.38 (26 Jun 2011) + + 26 Jun 2011; Justin Lecher -gbrowse-2.26.ebuild, + -files/GBrowseInstall.pm-2.26.patch, + -files/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm-2.26.patc= h, + -gbrowse-2.33.ebuild, -files/GBrowseInstall.pm-2.33.patch, + +gbrowse-2.38.ebuild, +files/GBrowseInstall.pm-2.38.patch: + Version Bump + 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 diff --git a/sci-biology/gbrowse/files/GBrowseInstall.pm-2.26.patch b/sci= -biology/gbrowse/files/GBrowseInstall.pm-2.26.patch deleted file mode 100644 index 4c17f8d..0000000 --- a/sci-biology/gbrowse/files/GBrowseInstall.pm-2.26.patch +++ /dev/null @@ -1,72 +0,0 @@ ---- install_util/GBrowseInstall.pm.ori 2010-11-27 12:01:58.000000000 +01= 00 -+++ install_util/GBrowseInstall.pm 2010-11-27 12:02:15.000000000 +0100 -@@ -436,8 +436,8 @@ - $self->ownership_warning($databases,$user); - } -=20 -- chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d= ','gbrowse-slave'); -- $self->fix_selinux; -+ # chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init= .d','gbrowse-slave'); -+ # $self->fix_selinux; -=20 - my $base =3D basename($self->install_path->{htdocs}); -=20 ---- install_util/GBrowseInstall.pm.ori 2011-02-14 13:39:46.000000000 +01= 00 -+++ install_util/GBrowseInstall.pm 2011-02-14 13:41:50.000000000 +0100 -@@ -438,25 +438,25 @@ - $gid =3D~ /^(\d+)$/; - $gid =3D $1; - =20 -- unless (chown $uid,$gid,$tmp) { -- $self->ownership_warning($tmp,$user); -- } -+# unless (chown $uid,$gid,$tmp) { -+# $self->ownership_warning($tmp,$user); -+# } -=20 - my $htdocs_i =3D File::Spec->catfile($self->install_path->{htdocs},= 'i'); - my $images =3D File::Spec->catfile($tmp,'images'); - my $htdocs =3D $self->install_path->{htdocs}; -- chown $uid,-1,$htdocs; -- { -- local $> =3D $uid; -- symlink($images,$htdocs_i); # so symlinkifowner match works! -- } -- chown $>,-1,$self->install_path->{htdocs}; -+# chown $uid,-1,$htdocs; -+# { -+# local $> =3D $uid; -+# symlink($images,$htdocs_i); # so symlinkifowner match works! -+# } -+# chown $>,-1,$self->install_path->{htdocs}; -=20 - my $databases =3D $self->install_path->{'databases'}; - =20 -- unless (chown $uid,$gid,glob(File::Spec->catfile($databases,'').'*'= )) { -- $self->ownership_warning($databases,$user); -- } -+# unless (chown $uid,$gid,glob(File::Spec->catfile($databases,'').'*= ')) { -+# $self->ownership_warning($databases,$user); -+# } -=20 - # chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init= .d','gbrowse-slave'); - # $self->fix_selinux; ---- install_util/GBrowseInstall.pm.ori 2011-02-14 13:50:41.000000000 +01= 00 -+++ install_util/GBrowseInstall.pm 2011-02-14 13:51:46.000000000 +0100 -@@ -470,11 +470,11 @@ - my @inc =3D map{"-I$_"} split ':',$self->added_to_INC; - system $perl,@inc,$metadb_script; -=20 -- if (Module::Build->y_n( -- "It is recommended that you restart Apache. Shall I try this for y= ou?",'y' -- )) { -- system "sudo /etc/init.d/apache2 restart"; -- } -+# if (Module::Build->y_n( -+# "It is recommended that you restart Apache. Shall I try this for = you?",'y' -+# )) { -+# system "sudo /etc/init.d/apache2 restart"; -+# } - =20 - print STDERR "\n***INSTALLATION COMPLETE***\n"; - print STDERR "Load http://localhost/$base for demo and documentatio= n.\n"; diff --git a/sci-biology/gbrowse/files/GBrowseInstall.pm-2.33.patch b/sci= -biology/gbrowse/files/GBrowseInstall.pm-2.38.patch similarity index 100% rename from sci-biology/gbrowse/files/GBrowseInstall.pm-2.33.patch rename to sci-biology/gbrowse/files/GBrowseInstall.pm-2.38.patch diff --git a/sci-biology/gbrowse/files/GBrowseInstall.pm-disable-gbrowse_= metadb_config.pl.pm-2.26.patch b/sci-biology/gbrowse/files/GBrowseInstall= .pm-disable-gbrowse_metadb_config.pl.pm-2.26.patch deleted file mode 100644 index 0dde704..0000000 --- a/sci-biology/gbrowse/files/GBrowseInstall.pm-disable-gbrowse_metadb_= config.pl.pm-2.26.patch +++ /dev/null @@ -1,21 +0,0 @@ ---- install_util/GBrowseInstall.pm.ori 2011-05-11 04:10:08.000000000 +02= 00 -+++ install_util/GBrowseInstall.pm 2011-05-11 04:10:26.000000000 +0200 -@@ -463,12 +463,12 @@ -=20 - my $base =3D basename($self->install_path->{htdocs}); -=20 -- # Configure the databases, if needed. -- print STDERR "Updating user account database...\n"; -- my $metadb_script =3D File::Spec->catfile("bin", "gbrowse_metadb_co= nfig.pl"); -- my $perl =3D $self->perl; -- my @inc =3D map{"-I$_"} split ':',$self->added_to_INC; -- system $perl,@inc,$metadb_script; -+# # Configure the databases, if needed. -+# print STDERR "Updating user account database...\n"; -+# my $metadb_script =3D File::Spec->catfile("bin", "gbrowse_metadb_c= onfig.pl"); -+# my $perl =3D $self->perl; -+# my @inc =3D map{"-I$_"} split ':',$self->added_to_INC; -+# system $perl,@inc,$metadb_script; -=20 - # if (Module::Build->y_n( - # "It is recommended that you restart Apache. Shall I try this for = you?",'y' diff --git a/sci-biology/gbrowse/gbrowse-2.26.ebuild b/sci-biology/gbrows= e/gbrowse-2.26.ebuild deleted file mode 100644 index 363d18d..0000000 --- a/sci-biology/gbrowse/gbrowse-2.26.ebuild +++ /dev/null @@ -1,170 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ -EAPI=3D"2" - -inherit perl-module webapp - -MY_P=3D"GBrowse-${PV}" - -DESCRIPTION=3D"Display of genomic annotations on interactive web pages" -HOMEPAGE=3D"http://gmod.org/" -SRC_URI=3D" - mirror://sourceforge/gmod/${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 )" - -LICENSE=3D"Artistic" -# webapp ebuilds do not set SLOT -KEYWORDS=3D"~x86 ~amd64" -IUSE=3D"-minimal svg test" # 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) -# TODO: make sure www-servers/apache +cgi -DEPEND=3D" - >=3Ddev-lang/perl-5.8.8 - dev-perl/Capture-Tiny - >=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 - svg? ( dev-perl/GD-SVG )" - -# TODO: based on the following message in apache/error_log the list of d= eps should be longer -# GBROWSE NOTICE: To enable PDF generation, please enter the directory "= /home/httpd" and run the commands: "sudo mkdir .inkscape .gnome2" and "su= do chown apache .inkscape .gnome2". To turn off this message add "genera= te pdf =3D 0" to the [GENERAL] section of your GBrowse.conf configuration= file., referer: http://127.0.0.1/gbrowse/cgi-bin/gbrowse_details/yeast?r= ef=3DchrII;start=3D90739;end=3D92028;name=3DYBL069W;class=3DSequence;feat= ure_id=3D881;db_id=3Dannotations%3Adatabase - -# * Bio::DB::BigFile is not installed -# * Bio::DB::Sam is not installed -# * DBD::Pg is not installed - -RDEPEND=3D"${DEPEND} - >=3Dwww-servers/apache-2.0.47 - www-apache/mod_fastcgi - dev-perl/DBI - || ( dev-perl/DBD-Pg dev-perl/DBD-mysql ) - !minimal? ( - dev-perl/File-NFSLock - dev-perl/FCGI - perl-core/Math-BigInt - perl-core/Math-BigInt-FastCalc - dev-perl/Math-BigInt-GMP - dev-perl/Digest-SHA1 - dev-perl/Crypt-SSLeay - dev-perl/Net-SMTP-SSL - dev-perl/Net-OpenID-Consumer - virtual/perl-DB_File - dev-perl/DB_File-Lock - dev-perl/GD-SVG - dev-perl/Text-Shellwords - dev-perl/XML-Twig - dev-perl/XML-DOM - dev-perl/XML-Writer - dev-perl/XML-Parser - dev-perl/Bio-Das - dev-perl/Text-Shellwords - )" - -src_prepare() { - sed -i 's/return unless -t STDIN/return/' install_util/GBrowseInstall.p= m || die - sed -i 's/process_/bp_process_/g' INSTALL || die - epatch "${FILESDIR}"/GBrowseInstall.pm-"${PV}".patch || die "Failed to = patch" - epatch "${FILESDIR}"/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl= "${PV}".pm.patch || die "Failed to patch" -} - -src_configure() { - # GBROWSE_ROOT is the root path in SRC_URI to be prepended - # /usr/share/webapps/gbrowse/2.03/htdocs/etc/gbrowse/GBrowse.conf - - # if we use CONF=3D"${D}${MY_HTDOCSDIR}"/etc/gbrowse the the install pr= ocess - # will not find currently installed config files and therefore place *.= conf - # files into "{$S}"/blib/conf/*.conf instead of creating "{$S}"/blib/co= nf/*.conf.new - webapp_src_preinst - perl Makefile.PL \ - HTDOCS=3D"${MY_HTDOCSDIR}" \ - CGIBIN=3D"${MY_HTDOCSDIR}"/cgi-bin \ - CONF=3D"${MY_HTDOCSDIR}"/etc/gbrowse \ - PACKAGE_DIR=3D"${D}" \ - INSTALLDIRS=3Dvendor \ - GBROWSE_ROOT=3D"gbrowse" \ - DESTDIR=3D"${D}" \ - DATABASES=3D"/var/www/gbrowse2/databases/" \ - TMP=3D"/var/tmp/gbrowse2" \ - INSTALLETC=3D"n" \ - INSTALLCONF=3D"n" \ - WWWUSER=3D"apache" \ - DO_XS=3D1 \ - NONROOT=3D1 \ - || die - - #sed -i 's#DBI:SQLite:#DBI:SQLite:'${D}'#' "${S}"/install_util/GBrowseI= nstall.pm || die - #sed -i 's#DBI:SQLite:#DBI:SQLite:'${D}'#' "${S}"/conf/GBrowse.conf || = die - #sed -i 's#/var/www/gbrowse2/databases/#'${D}'/var/www/gbrowse2/databas= es/#' "${S}"/_build/build_params - #sed -i 's#/var/www/gbrowse2/databases/#'${D}'/var/www/gbrowse2/databas= es/#' "${S}"/_build/config_data - #sed -i 's#/var/www/gbrowse2/databases/#'${D}'/var/www/gbrowse2/databas= es/#' "${S}"/_build/runtime_params -} - -src_install() { - mydoc=3D"Changes README TODO INSTALL" - perl-module_src_install - - # TODO: write our own readme - webapp_src_preinst - webapp_postinst_txt en "${S}"/INSTALL || die - webapp_src_install - - # should create a /etc/init.d/ startup script based on this - # /var/tmp/portage/sci-biology/gbrowse-2.03/work/GBrowse-2.03/etc/init.= d/gbrowse-slave - - # pre-create the directory so we can force its owner later on - mkdir -p "${D}"/var/www/gbrowse2/databases || die - chown -R apache.apache "${D}"/var/www/gbrowse2/databases || die - mkdir -p "${D}"/var/www/localhost/htdocs/gbrowse || die - - ln -s "${D}"/var/tmp/gbrowse2/images "${D}"/var/www/localhost/htdocs/gb= rowse/i || die - - einfo "Probably you want to install a cron job to remove the generated = temporary images:" - einfo "find /var/tmp/gbrowse2/images -type f -atime +20 -print -exec rm= {}" - - einfo "Make sure you compiled apache with +cgi and copy ${FILESDIR}/gbr= owse.conf.vhosts.d to /etc/apache2/vhosts.d/" - - sed -i "s#"${D}"##g" "${S}"/install_util/GBrowseInstall.pm || die - sed -i "s#"${D}"##" "${S}"/blib/conf/GBrowse.conf* - sed -i 's#DBI:SQLite:'${D}'/var/www/gbrowse2/databases/#DBI:SQLite:/var= /www/gbrowse2/databases/#' "${S}"/install_util/GBrowseInstall.pm || die -} - -pkg_postinst() { - webapp_pkg_postinst || die "webapp_pkg_postinst failed" - - einfo "Please run gbrowse_metadb_config.pl to upate SQlite flatfiles or= the live database" - einfo "This was disabled by "${FILESDIR}"/GBrowseInstall.pm-disable-gbr= owse_metadb_config.pl.pm.patch" -} - -src_test() { - mysql -uroot -p password -e 'create database yeast' - mysql -uroot -p password -e 'grant all privileges on yeast.* to gbrowse= @localhost' - mysql -uroot -p password -e 'grant file on *.* to gbrowse@localhost' - mysql -uroot -p password -e 'grant select on yeast.* to nobody@localhos= t' - - cd /usr/portage/distfiles || die - gzip -d yeast.fasta.gz || die - gzip -d yeast.gff.gz || die - #gzip -d fly.fasta.gz - #gzip -d fly.gff.gz - bp_bulk_load_gff.pl -d yeast -fasta yeast.fasta yeast.gff || die -} diff --git a/sci-biology/gbrowse/gbrowse-2.33.ebuild b/sci-biology/gbrows= e/gbrowse-2.38.ebuild similarity index 100% rename from sci-biology/gbrowse/gbrowse-2.33.ebuild rename to sci-biology/gbrowse/gbrowse-2.38.ebuild