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 1Pp0fZ-0005bP-FK for garchives@archives.gentoo.org; Mon, 14 Feb 2011 15:48:57 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 0DB5DE0B5A; Mon, 14 Feb 2011 15:48:50 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id C2DC9E0B78 for ; Mon, 14 Feb 2011 15:48:50 +0000 (UTC) Received: from pelican.gentoo.org (unknown [66.219.59.40]) (using TLSv1 with cipher ADH-CAMELLIA256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 1CD491B41D3 for ; Mon, 14 Feb 2011 15:48:50 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by pelican.gentoo.org (Postfix) with ESMTP id 171928006A for ; Mon, 14 Feb 2011 15:48:49 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <2cd3f93dfd0672f228900dd9584f57f573fbdc46.mmokrejs@gentoo> 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/files/GBrowseInstall.pm.patch sci-biology/gbrowse/gbrowse-2.03.ebuild sci-biology/gbrowse/gbrowse-2.26.ebuild X-VCS-Directories: sci-biology/gbrowse/files/ sci-biology/gbrowse/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 2cd3f93dfd0672f228900dd9584f57f573fbdc46 Date: Mon, 14 Feb 2011 15:48:49 +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: a3b358a9c925d54c1eebc867130a8b84 commit: 2cd3f93dfd0672f228900dd9584f57f573fbdc46 Author: Martin Mokrejs gentoo org> AuthorDate: Mon Feb 14 15:30:31 2011 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Mon Feb 14 15:30:31 2011 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=3Dproj/sci.git;a=3Dc= ommit;h=3D2cd3f93d sci-biology/gbrowse: version bump, more DEPS added, tiny webappconfig imp= rovement (Portage version: 2.1.9.28/git/Linux i686, unsigned Manifest commit) --- sci-biology/gbrowse/files/GBrowseInstall.pm.patch | 63 ++++++++++++++= +++++- .../{gbrowse-2.03.ebuild =3D> gbrowse-2.26.ebuild} | 16 +++++- 2 files changed, 76 insertions(+), 3 deletions(-) diff --git a/sci-biology/gbrowse/files/GBrowseInstall.pm.patch b/sci-biol= ogy/gbrowse/files/GBrowseInstall.pm.patch index e6163a7..863930e 100644 --- a/sci-biology/gbrowse/files/GBrowseInstall.pm.patch +++ b/sci-biology/gbrowse/files/GBrowseInstall.pm.patch @@ -1,5 +1,5 @@ ---- GBrowse-2.03/install_util/GBrowseInstall.pm.ori 2010-11-27 12:01:58.= 000000000 +0100 -+++ GBrowse-2.03/install_util/GBrowseInstall.pm 2010-11-27 12:02:15.0000= 00000 +0100 +--- GBrowse-2.26/install_util/GBrowseInstall.pm.ori 2010-11-27 12:01:58.= 000000000 +0100 ++++ GBrowse-2.26/install_util/GBrowseInstall.pm 2010-11-27 12:02:15.0000= 00000 +0100 @@ -436,8 +436,8 @@ $self->ownership_warning($databases,$user); } @@ -11,3 +11,62 @@ =20 my $base =3D basename($self->install_path->{htdocs}); =20 +--- GBrowse-2.26/install_util/GBrowseInstall.pm.ori 2011-02-14 13:39:46.= 000000000 +0100 ++++ GBrowse-2.26/install_util/GBrowseInstall.pm 2011-02-14 13:41:50.0000= 00000 +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'); + # $self->fix_selinux; +--- GBrowse-2.26/install_util/GBrowseInstall.pm.ori 2011-02-14 13:50:41.= 000000000 +0100 ++++ GBrowse-2.26/install_util/GBrowseInstall.pm 2011-02-14 13:51:46.0000= 00000 +0100 +@@ -470,11 +470,11 @@ + my @inc =3D map{"-I$_"} 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/$base for demo and documentatio= n.\n"; diff --git a/sci-biology/gbrowse/gbrowse-2.03.ebuild b/sci-biology/gbrows= e/gbrowse-2.26.ebuild similarity index 93% rename from sci-biology/gbrowse/gbrowse-2.03.ebuild rename to sci-biology/gbrowse/gbrowse-2.26.ebuild index 9fc872b..b525bcc 100644 --- a/sci-biology/gbrowse/gbrowse-2.03.ebuild +++ b/sci-biology/gbrowse/gbrowse-2.26.ebuild @@ -31,6 +31,7 @@ S=3D"${WORKDIR}/${MY_P}" # TODO: dev-perl/MOBY, dev-perl/Bio-SCF, dev-perl/Safe-World (not compat= ible w/perl-5.10) # TODO: make sure www-servers/apache +cgi DEPEND=3D">=3Ddev-lang/perl-5.8.8 + dev-perl/Capture-Tiny >=3Dsci-biology/bioperl-1.6 >=3Ddev-perl/GD-2.07 dev-perl/IO-String @@ -45,6 +46,11 @@ DEPEND=3D">=3Ddev-lang/perl-5.8.8 # TODO: based on the following message in apache/error_log the list of d= eps should be longer # GBROWSE NOTICE: To enable PDF generation, please enter the directory "= /home/httpd" and run the commands: "sudo mkdir .inkscape .gnome2" and "su= do chown apache .inkscape .gnome2". To turn off this message add "genera= te pdf =3D 0" to the [GENERAL] section of your GBrowse.conf configuration= file., referer: http://127.0.0.1/gbrowse/cgi-bin/gbrowse_details/yeast?r= ef=3DchrII;start=3D90739;end=3D92028;name=3DYBL069W;class=3DSequence;feat= ure_id=3D881;db_id=3Dannotations%3Adatabase =20 +# * Bio::DB::BigFile is not installed +# * Bio::DB::Sam is not installed +# * DBD::Pg is not installed + + RDEPEND=3D"${DEPEND} >=3Dwww-servers/apache-2.0.47 www-apache/mod_fastcgi @@ -54,6 +60,8 @@ RDEPEND=3D"${DEPEND} dev-perl/File-NFSLock dev-perl/FCGI perl-core/Math-BigInt + perl-core/Math-BigInt-FastCalc + dev-perl/Math-BigInt-GMP dev-perl/Digest-SHA1 dev-perl/Crypt-SSLeay dev-perl/Net-SMTP-SSL @@ -67,6 +75,7 @@ RDEPEND=3D"${DEPEND} dev-perl/XML-Writer dev-perl/XML-Parser dev-perl/Bio-Das + dev-perl/Text-Shellwords )" =20 src_prepare() { @@ -93,6 +102,7 @@ src_configure() { INSTALLCONF=3D"n" \ WWWUSER=3D"apache" \ DO_XS=3D1 \ + NONROOT=3D1 \ || die } =20 @@ -102,7 +112,7 @@ src_install() { =20 # TODO: write our own readme webapp_postinst_txt en "${S}"/INSTALL - webapp_src_install + webapp_src_install || die "Failed running webapp_src_install" =20 # 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 @@ -118,6 +128,10 @@ src_install() { einfo "Make sure you compiled apache with +cgi and copy ${FILESDIR}/gbr= owse.conf.vhosts.d to /etc/apache2/vhosts.d/" } =20 +pkg_postinst() { + webapp_pkg_postinst || die "webapp_pkg_postinst failed" +} + src_test() { mysql -uroot -p password -e 'create database yeast' mysql -uroot -p password -e 'grant all privileges on yeast.* to gbrowse= @localhost'