proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

4 files changed, 153 insertions, 0 deletions

diff --git a/sci-biology/GBrowse/GBrowse-2.48-r1.ebuild b/sci-biology/GBrowse/GBrowse-2.48-r1.ebuild
new file mode 100644
index 00000000000..a3c0228b819
--- /dev/null
+++ b/sci-biology/GBrowse/GBrowse-2.48-r1.ebuild
@@ -0,0 +1,72 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+MODULE_AUTHOR=LDS
+inherit perl-module webapp
+
+DESCRIPTION="Generic Model Organism Database Project - The Generic Genome Browser"
+HOMEPAGE="http://gmod.org/wiki/GBrowse"
+KEYWORDS="~amd64 ~x86"
+IUSE="-minimal mysql postgres +sqlite"
+
+SLOT="0"
+WEBAPP_MANUAL_SLOT="yes"
+
+CDEPEND="!<sci-biology/GBrowse-2.44-r1
+	>=sci-biology/bioperl-1.6.9
+	>=dev-perl/Bio-Graphics-2.09
+	>=dev-perl/GD-2.07
+	>=dev-perl/CGI-Session-4.02
+	dev-perl/IO-String
+	dev-perl/JSON
+	dev-perl/libwww-perl
+	dev-perl/Statistics-Descriptive
+	!minimal? (
+		dev-perl/Bio-Das
+		>=dev-perl/Bio-SamTools-1.20
+		dev-perl/Crypt-SSLeay
+		dev-perl/DB_File-Lock
+		dev-perl/DBI
+		mysql? ( dev-perl/DBD-mysql )
+		postgres? ( dev-perl/DBD-Pg )
+		sqlite? ( dev-perl/DBD-SQLite )
+		dev-perl/FCGI
+		dev-perl/File-NFSLock
+		dev-perl/GD-SVG
+		dev-perl/Net-OpenID-Consumer
+		dev-perl/Net-SMTP-SSL
+	)"
+#		>=dev-perl/Bio-DB-BigFile-1.00 - requires jklib to compile
+DEPEND="dev-perl/Module-Build
+	dev-perl/Capture-Tiny
+	${CDEPEND}"
+RDEPEND="${CDEPEND}"
+
+PATCHES=( "${FILESDIR}"/GBrowseInstall.pm-2.39.patch )
+
+src_configure() {
+	webapp_src_preinst
+
+#	myconf="--install_base=${D}/usr" or "--install_base=/opt/gbrowse"
+	myconf="--conf=/etc/gbrowse2"
+	myconf="${myconf} --htdocs=${MY_HTDOCSDIR}"
+	myconf="${myconf} --cgibin=${MY_CGIBINDIR}"
+	myconf="${myconf} --tmp=/var/tmp/gbrowse2"
+	myconf="${myconf} --persistent=/var/db/gbrowse2"
+	myconf="${myconf} --databases=/var/db/gbrowse2/databases"
+	myconf="${myconf} --installconf=no"
+	myconf="${myconf} --installetc=no"
+	perl-module_src_configure
+}
+
+src_install() {
+	dodir /var/tmp/gbrowse2
+	dodir /var/db/gbrowse2/sessions
+	dodir /var/db/gbrowse2/userdata
+	webapp_serverowned -R /var/tmp/gbrowse2 /var/db/gbrowse2
+	perl-module_src_install
+	webapp_src_install
+}
diff --git a/sci-biology/GBrowse/Manifest b/sci-biology/GBrowse/Manifest
new file mode 100644
index 00000000000..204fe59d5aa
--- /dev/null
+++ b/sci-biology/GBrowse/Manifest
@@ -0,0 +1 @@
+DIST GBrowse-2.48.tar.gz 11958127 SHA256 02772c5a7a31ed87733e21278efec2edd3bd6ee8a4bec9b002233e57f6dc9681 SHA512 d5a07caf1517fb15741e8e6056669763eb04678a42637a9e90788c91e74fb34515b5f86aac10a00f29d8848aceb19d6f5f7258d2dda0e281feee550e9e2fb3db WHIRLPOOL 5a3ec31de1582c4c551c76908ca8e8024c8d3311404f0c94f7b75a391c340da0ededd80df34be3f10f581902ba1408d84e3e65218f46322546623e15a1020135
diff --git a/sci-biology/GBrowse/files/GBrowseInstall.pm-2.39.patch b/sci-biology/GBrowse/files/GBrowseInstall.pm-2.39.patch
new file mode 100644
index 00000000000..5aa0be9df91
--- /dev/null
+++ b/sci-biology/GBrowse/files/GBrowseInstall.pm-2.39.patch
@@ -0,0 +1,72 @@
+diff -durr GBrowse-2.39-orig/install_util/GBrowseInstall.pm GBrowse-2.39/install_util/GBrowseInstall.pm
+--- GBrowse-2.39-orig/install_util/GBrowseInstall.pm	2011-07-19 20:14:52.434608020 +0000
++++ GBrowse-2.39/install_util/GBrowseInstall.pm	2011-07-19 21:02:13.685107753 +0000
+@@ -454,33 +454,33 @@
+     $gid =~ /^(\d+)$/;
+     $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;
++#    chown $uid,-1,$htdocs;
+     {
+ 	local $> = $uid;
+-	symlink($images,$htdocs_i);  # so symlinkifowner match works!
++#	symlink($images,$htdocs_i);  # so symlinkifowner match works!
+     }
+-    chown $>,-1,$self->install_path->{htdocs};
++#    chown $>,-1,$self->install_path->{htdocs};
+ 
+     my $persistent = $self->install_path->{'persistent'};
+     my $sessions   = File::Spec->catfile($persistent,'sessions');
+     my $userdata   = File::Spec->catfile($persistent,'userdata');
+-    mkpath([$sessions,$userdata],0711);
++#    mkpath([$sessions,$userdata],0711);
+ 
+     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');
+-    $self->fix_selinux;
++    # chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave');
++    # $self->fix_selinux;
+ 
+     my $base = basename($self->install_path->{htdocs});
+ 
+@@ -489,14 +489,14 @@
+     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;
+-    system 'sudo','chown','-R',"$uid.$gid",$sessions,$userdata;
++#    system $perl,@inc,$metadb_script;
++#    system 'sudo','chown','-R',"$uid.$gid",$sessions,$userdata;
+ 
+-    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";
+Only in GBrowse-2.39/install_util: GBrowseInstall.pm~
diff --git a/sci-biology/GBrowse/metadata.xml b/sci-biology/GBrowse/metadata.xml
new file mode 100644
index 00000000000..32b15c723f9
--- /dev/null
+++ b/sci-biology/GBrowse/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci-biology</herd>
+<upstream>
+  <remote-id type="cpan">GBrowse</remote-id>
+</upstream>
+</pkgmetadata>