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

[Martin Mokrejs]

commit:     bfc8451b06a8727456543751d139d29706473c03
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 17 18:11:07 2012 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 17 18:11:07 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bfc8451b

version bump and some fixes so that it works with webappconfig again?

(Portage version: 2.1.10.44/git/Linux i686, unsigned Manifest commit)

---
 sci-biology/gbrowse/ChangeLog                      |    6 +
 .../gbrowse/files/GBrowseInstall.pm-2.45.patch     |   32 +++
 sci-biology/gbrowse/gbrowse-2.45.ebuild            |  199 ++++++++++++++++++++
 3 files changed, 237 insertions(+), 0 deletions(-)

diff --git a/sci-biology/gbrowse/ChangeLog b/sci-biology/gbrowse/ChangeLog
index c63914a..41e2334 100644
--- a/sci-biology/gbrowse/ChangeLog
+++ b/sci-biology/gbrowse/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2012 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-2.45 (17 Jan 2012)
+
+  17 Jan 2012; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
+  +gbrowse-2.45.ebuild, +files/GBrowseInstall.pm-2.45.patch:
+  version bump and some fixes so that it works with webappconfig again?
+
   17 Jan 2012; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
   gbrowse-2.39.ebuild:
   added dev-perl/TermReadKey to dependencies

diff --git a/sci-biology/gbrowse/files/GBrowseInstall.pm-2.45.patch b/sci-biology/gbrowse/files/GBrowseInstall.pm-2.45.patch
new file mode 100644
index 0000000..e91fe16
--- /dev/null
+++ b/sci-biology/gbrowse/files/GBrowseInstall.pm-2.45.patch
@@ -0,0 +1,32 @@
+--- 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 13:50:41.000000000 +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/gbrowse-2.45.ebuild b/sci-biology/gbrowse/gbrowse-2.45.ebuild
new file mode 100644
index 0000000..f914844
--- /dev/null
+++ b/sci-biology/gbrowse/gbrowse-2.45.ebuild
@@ -0,0 +1,199 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+EAPI="2"
+
+inherit perl-module webapp
+
+MY_P="GBrowse-${PV}"
+
+DESCRIPTION="Display of genomic annotations on interactive web pages"
+HOMEPAGE="http://gmod.org/"
+# mirror://sourceforge/gmod/${MY_P}.tar.gz
+# mirror://cpan/authors/id/L/LD/LDS/GBrowse-2.33.tar.gz
+SRC_URI="
+	mirror://cpan/authors/id/L/LD/LDS/${MY_P}.tar.gz
+	test? (
+		http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/saccharomyces_cerevisiae.gff.bz2
+		http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/Refseq_Genome_TBLASTX.tar.gz
+		http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/README-gff-files
+		http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/human.gff.tar.gz
+		http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.fasta.gz
+		http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.gff.gz
+		http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.fasta.gz
+		http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.gff.gz
+		http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.fasta.gz
+		http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.gff.gz )"
+
+LICENSE="Artistic"
+# webapp ebuilds do not set SLOT
+KEYWORDS="~x86 ~amd64"
+IUSE="cgi fastcgi minimal mysql pdf postgres svg test" # lwp moby scf
+
+S="${WORKDIR}/${MY_P}"
+
+# TODO: dev-perl/MOBY, dev-perl/Bio-SCF, dev-perl/Safe-World (not compatible w/perl-5.10)
+# how about mod_fcgi and dev-libs/fcgi and mod_scgi?
+DEPEND="!!sci-biology/GBrowse
+	>=perl-core/Module-Build-0.380.0
+	>=dev-lang/perl-5.8.8
+	dev-perl/Capture-Tiny
+	>=sci-biology/bioperl-1.6.901
+	>=dev-perl/GD-2.07
+	dev-perl/IO-String
+	virtual/perl-Digest-MD5
+	>=dev-perl/CGI-Session-4.03
+	dev-perl/Statistics-Descriptive
+	>=dev-perl/Bio-Graphics-1.97
+	>=dev-perl/JSON-2.510.0
+	dev-perl/TermReadKey
+	dev-perl/libwww-perl
+	svg? ( dev-perl/GD-SVG )
+	pdf? ( media-gfx/inkscape )
+	mysql? ( dev-perl/DBD-mysql )
+	postgres? ( dev-perl/DBD-Pg )
+	sci-biology/ucsc-genome-browser" # that provides bigWig.h and jkweb.a, aka Jim Kent's src
+
+# TODO: based on the following message in apache/error_log the list of deps should be longer
+# GBROWSE NOTICE: To enable PDF generation, please enter the directory "/home/httpd" and run the commands: "sudo mkdir .inkscape .gnome2" and "sudo chown apache .inkscape .gnome2".  To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://127.0.0.1/gbrowse/cgi-bin/gbrowse_details/yeast?ref=chrII;start=90739;end=92028;name=YBL069W;class=Sequence;feature_id=881;db_id=annotations%3Adatabase
+
+RDEPEND="${DEPEND}
+	>=www-servers/apache-2.0.47
+	fastcgi? ( dev-libs/fcgi )
+	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
+		postgres? ( >=dev-perl/Bio-DB-Das-Chado-0.32 )
+		>=dev-perl/Bio-SamTools-1.29
+		>=dev-perl/Bio-BigFile-1.06
+	)"
+
+src_prepare() {
+	sed -i 's/return unless -t STDIN/return/' install_util/GBrowseInstall.pm || die "Failed to kill the interactive behavior of install_util/GBrowseInstall.pm"
+	sed -i 's/process_/bp_process_/g' INSTALL || die "Failed to prepend bp_ prefix to INSTALL file"
+	epatch "${FILESDIR}"/GBrowseInstall.pm-"${PV}".patch || die "Failed to apply GBrowseInstall.pm-"${PV}".patch"
+	epatch "${FILESDIR}"/destdir.patch || die "Failed to apply destdir.patch"
+	epatch "${FILESDIR}"/fix-PNG-export.patch || die "Failed to apply fix-PNG-export.patch"
+	epatch "${FILESDIR}"/symlink.patch || die "Failed to apply symlink.patch"
+	epatch "${FILESDIR}"/gbrowse_metadb_config.pl.patch || die "Failed to apply gbrowse_metadb_config.pl.patch"
+	epatch "${FILESDIR}"/disable-gbrowse_metadb_config.pl.patch || die "Failed to apply disable-gbrowse_metadb_config.pl.patch"
+	for f in conf/synteny/wild_rice_synteny.conf conf/synteny/rice_synteny.conf conf/GBrowse.conf \
+			htdocs/tutorial/tutorial.html htdocs/index.html lib/Bio/Graphics/Browser2/Action.pm \
+			Changes; do
+		sed -i 's#/var/lib/gbrowse2#/var/db/gbrowse2#' $f || die "Failed to rewrite /var/lib/gbrowse2 to /var/db/gbrowse2 in $f"
+	done
+	for f in htdocs/index.html; do
+		sed -i 's#/usr/lib/cgi-bin/gb2#/usr/share/webapps/gbrowse/"${PV}"/htdocs/cgi-bin#' $f || die "Failed to rewrite /usr/lib/cgi-bin/gb2 to /usr/share/webapps/gbrowse/"${PV}"/htdocs/cgi-bin in $f"
+	done
+}
+
+src_configure() {
+	# GBROWSE_ROOT is the root path in SRC_URI to be prepended
+	# /usr/share/webapps/gbrowse/2.03/htdocs/etc/gbrowse/GBrowse.conf
+	webapp_src_preinst
+	perl Makefile.PL \
+		HTDOCS="${MY_HTDOCSDIR}" \
+		CGIBIN="${MY_HTDOCSDIR}"/cgi-bin \
+		CONF="${MY_HTDOCSDIR}"/etc/gbrowse \
+		PACKAGE_DIR="${D}" \
+		INSTALLDIRS=vendor \
+		GBROWSE_ROOT="gbrowse" \
+		DESTDIR="${D}" \
+		DATABASES="/var/db/gbrowse2/databases" \
+		PERSISTENT="/var/db/gbrowse2" \
+		TMP="/var/tmp/gbrowse2" \
+		INSTALLETC="n" \
+		INSTALLCONF="n" \
+		WWWUSER="apache" \
+		DO_XS=1 \
+		NONROOT=1 \
+		|| die
+}
+
+src_install() {
+	mydoc="Changes README TODO INSTALL"
+	perl-module_src_install
+
+	# TODO: write our own readme
+	webapp_postinst_txt en "${S}"/INSTALL
+	webapp_src_install || die "Failed running webapp_src_install"
+
+	# should create a /etc/init.d/ startup script based on this
+	# /var/tmp/portage/sci-biology/gbrowse-2.03/work/GBrowse-2.03/etc/init.d/gbrowse-slave
+
+	mkdir -p "${D}"/var/tmp/gbrowse2/images
+	chown -R apache.apache "${D}"/var/tmp/gbrowse2
+
+	# mkdir -p "${D}"/var/www/localhost/htdocs/gbrowse || die
+	# ln -s "${D}"/var/tmp/gbrowse2/images "${D}"/usr/share/webapps/gbrowse/"${PV}"/htdocs/i || die
+
+	# whole "${D}"/var/db/gbrowse2 has to be owned by apache.apache otherwise:
+	#  1. you hit an error that /var/db/gbrowse2/sessions/cgisess.db.lck
+	#		[no, it is not enough chown -R apache.apache /var/db/gbrowse2/sessions, the parent dir has to be apapche.apache as well]
+	# 2. even if you set /var/db/gbrowse2 to apache.apache still it is not enough, you will get
+	# 		[Tue Jan 17 14:59:40 2012] [error] [client 127.0.0.1] Use of uninitialized value $label in lc at /usr/lib/perl5/vendor_perl/5.12.4/i686-linux-thread-multi/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm line 34., referer: http://127.0.0.1/gbrowse/cgi-bin/gbrowse/yeast/
+
+	mkdir -p "${D}"/var/db/gbrowse2
+	mkdir -p "${D}"/var/db/gbrowse2/databases
+	mkdir -p "${D}"/var/db/gbrowse2/sessions "${D}"/var/db/gbrowse2/userdata
+	chown -R apache.apache "${D}"/var/db/gbrowse2 # it has to be owned by apache.apache otherwise /var/db/gbrowse2/sessions/cgisess.db.lck cannot be created although /var/db/gbrowse2/sessions is owner by apache.apache
+
+	einfo "Dropping trailing 'databases' from db_variable in conf/GBrowse.conf"
+	sed -i 's#/var/db/gbrowse2/databases#/var/db/gbrowse2#' conf/GBrowse.conf || die "Failed to dropping trailing 'databases' from db_variable in conf/GBrowse.conf"
+
+	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 do"
+	einfo "cp -i ${FILESDIR}/gbrowse.conf.vhosts.d /etc/apache2/vhosts.d/gbrowse.conf"
+
+	sed -i "s#"${D}"##g" "${S}"/install_util/GBrowseInstall.pm || die
+	sed -i "s#"${D}"##" "${S}"/blib/conf/GBrowse.conf*
+	sed -i 's#DBI:SQLite:'${D}'/var/lib/gbrowse2/databases/#DBI:SQLite:/var/db/gbrowse2/databases/#' "${S}"/install_util/GBrowseInstall.pm || die
+}
+
+pkg_postinst() {
+	webapp_pkg_postinst || die "webapp_pkg_postinst failed"
+
+	einfo "Please run gbrowse_metadb_config.pl to update SQLite flatfiles of the live database."
+	einfo "d='/usr/share/webapps/gbrowse/${PV}/htdocs/etc/gbrowse'; for f in \$d/*.conf.new; do \ "
+	einfo "		mv -i \$f \$d/\`basename \$f .new\`; done"
+
+	einfo "Fix also the other copy of the file:"
+	einfo "d='/var/www/localhost/htdocs/gbrowse/etc/gbrowse'; for f in \$d/*.conf.new; do \ "
+	einfo "     mv -i \$f \$d/\`basename \$f .new\`; done"
+}
+
+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
+}