[gentoo-commits] proj/sci:master commit in: sci-biology/gbrowse/files/, sci-biology/gbrowse/

[Justin Lecher]

commit:     a50c105c259094c0b358fb024a326dccc3751247
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 26 08:02:44 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jun 26 08:02:44 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a50c105c

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 => 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 => gbrowse-2.38.ebuild}   |    0
 6 files changed, 9 insertions(+), 263 deletions(-)

diff --git a/sci-biology/gbrowse/ChangeLog b/sci-biology/gbrowse/ChangeLog
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/ChangeLog,v 1.10 2007/07/29 17:07:38 phreak Exp $
 
+*gbrowse-2.38 (26 Jun 2011)
+
+  26 Jun 2011; Justin Lecher <jlec@g.o> -gbrowse-2.26.ebuild,
+  -files/GBrowseInstall.pm-2.26.patch,
+  -files/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm-2.26.patch,
+  -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 <jlec@g.o> -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

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 +0100
-+++ install_util/GBrowseInstall.pm	2010-11-27 12:02:15.000000000 +0100
-@@ -436,8 +436,8 @@
- 	$self->ownership_warning($databases,$user);
-     }
- 
--    chmod 0755,File::Spec->catfile($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;
- 
-     my $base = basename($self->install_path->{htdocs});
- 
---- install_util/GBrowseInstall.pm.ori	2011-02-14 13:39:46.000000000 +0100
-+++ install_util/GBrowseInstall.pm	2011-02-14 13:41:50.000000000 +0100
-@@ -438,25 +438,25 @@
-     $gid =~ /^(\d+)$/;
-     $gid = $1;
-     
--    unless (chown $uid,$gid,$tmp) {
--	$self->ownership_warning($tmp,$user);
--    }
-+#   unless (chown $uid,$gid,$tmp) {
-+#	$self->ownership_warning($tmp,$user);
-+#   }
- 
-     my $htdocs_i = File::Spec->catfile($self->install_path->{htdocs},'i');
-     my $images   = File::Spec->catfile($tmp,'images');
-     my $htdocs = $self->install_path->{htdocs};
--    chown $uid,-1,$htdocs;
--    {
--	local $> = $uid;
--	symlink($images,$htdocs_i);  # so symlinkifowner match works!
--    }
--    chown $>,-1,$self->install_path->{htdocs};
-+#    chown $uid,-1,$htdocs;
-+#    {
-+#	local $> = $uid;
-+#	symlink($images,$htdocs_i);  # so symlinkifowner match works!
-+#    }
-+#    chown $>,-1,$self->install_path->{htdocs};
- 
-     my $databases = $self->install_path->{'databases'};
-     
--    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,$user);
-+#    }
- 
-     # chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave');
-     # $self->fix_selinux;
---- install_util/GBrowseInstall.pm.ori	2011-02-14 13:50:41.000000000 +0100
-+++ install_util/GBrowseInstall.pm	2011-02-14 13:51:46.000000000 +0100
-@@ -470,11 +470,11 @@
-     my @inc           = map{"-I$_"} split ':',$self->added_to_INC;
-     system $perl,@inc,$metadb_script;
- 
--    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";
--    }
-+#    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";
-+#    }
-     
-     print STDERR "\n***INSTALLATION COMPLETE***\n";
-     print STDERR "Load http://localhost/$base for demo and documentation.\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 +0200
-+++ install_util/GBrowseInstall.pm	2011-05-11 04:10:26.000000000 +0200
-@@ -463,12 +463,12 @@
- 
-     my $base = basename($self->install_path->{htdocs});
- 
--    # Configure the databases, if needed.
--    print STDERR "Updating user account database...\n";
--    my $metadb_script = File::Spec->catfile("bin", "gbrowse_metadb_config.pl");
--    my $perl          = $self->perl;
--    my @inc           = map{"-I$_"} 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 = File::Spec->catfile("bin", "gbrowse_metadb_config.pl");
-+#    my $perl          = $self->perl;
-+#    my @inc           = map{"-I$_"} split ':',$self->added_to_INC;
-+#    system $perl,@inc,$metadb_script;
- 
- #    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/gbrowse/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="2"
-
-inherit perl-module webapp
-
-MY_P="GBrowse-${PV}"
-
-DESCRIPTION="Display of genomic annotations on interactive web pages"
-HOMEPAGE="http://gmod.org/"
-SRC_URI="
-	mirror://sourceforge/gmod/${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
-KEYWORDS="~x86 ~amd64"
-IUSE="-minimal svg test" # 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)
-# TODO: make sure www-servers/apache +cgi
-DEPEND="
-	>=dev-lang/perl-5.8.8
-	dev-perl/Capture-Tiny
-	>=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
-	svg? ( dev-perl/GD-SVG )"
-
-# 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
-
-#    *  Bio::DB::BigFile is not installed
-#    *  Bio::DB::Sam is not installed
-#    *  DBD::Pg is not installed
-
-RDEPEND="${DEPEND}
-	>=www-servers/apache-2.0.47
-	www-apache/mod_fastcgi
-	dev-perl/DBI
-	|| ( dev-perl/DBD-Pg dev-perl/DBD-mysql )
-	!minimal? (
-		dev-perl/File-NFSLock
-		dev-perl/FCGI
-		perl-core/Math-BigInt
-		perl-core/Math-BigInt-FastCalc
-		dev-perl/Math-BigInt-GMP
-		dev-perl/Digest-SHA1
-		dev-perl/Crypt-SSLeay
-		dev-perl/Net-SMTP-SSL
-		dev-perl/Net-OpenID-Consumer
-		virtual/perl-DB_File
-		dev-perl/DB_File-Lock
-		dev-perl/GD-SVG
-		dev-perl/Text-Shellwords
-		dev-perl/XML-Twig
-		dev-perl/XML-DOM
-		dev-perl/XML-Writer
-		dev-perl/XML-Parser
-		dev-perl/Bio-Das
-		dev-perl/Text-Shellwords
-	)"
-
-src_prepare() {
-	sed -i 's/return unless -t STDIN/return/' install_util/GBrowseInstall.pm || die
-	sed -i 's/process_/bp_process_/g' INSTALL || die
-	epatch "${FILESDIR}"/GBrowseInstall.pm-"${PV}".patch || die "Failed to patch"
-	epatch "${FILESDIR}"/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl"${PV}".pm.patch || die "Failed to patch"
-}
-
-src_configure() {
-	# GBROWSE_ROOT is the root path in SRC_URI to be prepended
-	# /usr/share/webapps/gbrowse/2.03/htdocs/etc/gbrowse/GBrowse.conf
-
-	# if we use CONF="${D}${MY_HTDOCSDIR}"/etc/gbrowse the the install process
-	# will not find currently installed config files and therefore place *.conf
-	# files into "{$S}"/blib/conf/*.conf instead of creating "{$S}"/blib/conf/*.conf.new
-	webapp_src_preinst
-	perl Makefile.PL \
-		HTDOCS="${MY_HTDOCSDIR}" \
-		CGIBIN="${MY_HTDOCSDIR}"/cgi-bin \
-		CONF="${MY_HTDOCSDIR}"/etc/gbrowse \
-		PACKAGE_DIR="${D}" \
-		INSTALLDIRS=vendor \
-		GBROWSE_ROOT="gbrowse" \
-		DESTDIR="${D}" \
-		DATABASES="/var/www/gbrowse2/databases/" \
-		TMP="/var/tmp/gbrowse2" \
-		INSTALLETC="n" \
-		INSTALLCONF="n" \
-		WWWUSER="apache" \
-		DO_XS=1 \
-		NONROOT=1 \
-		|| die
-
-	#sed -i 's#DBI:SQLite:#DBI:SQLite:'${D}'#' "${S}"/install_util/GBrowseInstall.pm || die
-	#sed -i 's#DBI:SQLite:#DBI:SQLite:'${D}'#' "${S}"/conf/GBrowse.conf || die
-	#sed -i 's#/var/www/gbrowse2/databases/#'${D}'/var/www/gbrowse2/databases/#' "${S}"/_build/build_params
-	#sed -i 's#/var/www/gbrowse2/databases/#'${D}'/var/www/gbrowse2/databases/#' "${S}"/_build/config_data
-	#sed -i 's#/var/www/gbrowse2/databases/#'${D}'/var/www/gbrowse2/databases/#' "${S}"/_build/runtime_params
-}
-
-src_install() {
-	mydoc="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/gbrowse/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 ${FILESDIR}/gbrowse.conf.vhosts.d to /etc/apache2/vhosts.d/"
-
-	sed -i "s#"${D}"##g" "${S}"/install_util/GBrowseInstall.pm || die
-	sed -i "s#"${D}"##" "${S}"/blib/conf/GBrowse.conf*
-	sed -i 's#DBI:SQLite:'${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-gbrowse_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@localhost'
-
-	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/gbrowse/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