gentoo resync : 12.05.2022

4 files changed, 0 insertions, 158 deletions

diff --git a/sci-biology/GBrowse/GBrowse-2.48-r1.ebuild b/sci-biology/GBrowse/GBrowse-2.48-r1.ebuild
deleted file mode 100644
index 2fcef3b41aff..000000000000
--- a/sci-biology/GBrowse/GBrowse-2.48-r1.ebuild
+++ /dev/null
@@ -1,71 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-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
deleted file mode 100644
index ddfd14a7c6fc..000000000000
--- a/sci-biology/GBrowse/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-AUX GBrowseInstall.pm-2.39.patch 2878 BLAKE2B 99ca47ef69aad80322bcc2f0a856a2e0e8d2185189172c842f3bfdc9efbda383f8d00ca5e6a829dbb48f1f668047ec4e66ac83cef433347453a91ee557820c1a SHA512 637dea799290213def1368cdb153463c96964ada99fd6c09d0b95e0d1e42a16942d66ef36282d39b92284ae6eb26c8346d5ad1289b5ec7b2196a1ba5090db85e
-DIST GBrowse-2.48.tar.gz 11958127 BLAKE2B e9527eb47302775d62e37990c42154b677284fff0f0f9624e9173e30e46c5aebbc8a02ee8dec0a1e98761812ef2363e0183008087bce4d283528b7935b4d5f91 SHA512 d5a07caf1517fb15741e8e6056669763eb04678a42637a9e90788c91e74fb34515b5f86aac10a00f29d8848aceb19d6f5f7258d2dda0e281feee550e9e2fb3db
-EBUILD GBrowse-2.48-r1.ebuild 1859 BLAKE2B c738aeb5114fc688fea7b2277332530452489c02309926a1acd7a5cde1225577a6c07e432f8aac8515c4d16c97962fbc0833807134292edfc0e3e4b4a768798e SHA512 e763f68e6c3d0d76284a68f918e39c00dfff5be6110852d6f9dde74072d8c1e686157a517c0a15a948bce679a77792d175acf1be1a93326c0e541f544e30086a
-MISC metadata.xml 328 BLAKE2B ce5ed72774e7d696776952832799cd960fae4bc4034e69d38db80fb3e9eceb77c538b0d6f15c0602582003cfe5e214124714e2e385d3d5707d2df8927b2a46ba SHA512 9bd9535f41bcb395c1d59abdbd4c9e0499aa6d945bf5a8fb79b1fe1b7d2e2864e3276878546160e238f1b04ecdfe95551f32f5d53587d85a8628f90d36ffdbc0
diff --git a/sci-biology/GBrowse/files/GBrowseInstall.pm-2.39.patch b/sci-biology/GBrowse/files/GBrowseInstall.pm-2.39.patch
deleted file mode 100644
index 5aa0be9df918..000000000000
--- a/sci-biology/GBrowse/files/GBrowseInstall.pm-2.39.patch
+++ /dev/null
@@ -1,72 +0,0 @@
-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
deleted file mode 100644
index 08238dd44f7a..000000000000
--- a/sci-biology/GBrowse/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<maintainer type="project">
-  <email>sci-biology@gentoo.org</email>
-  <name>Gentoo Biology Project</name>
-</maintainer>
-<upstream>
-  <remote-id type="cpan">GBrowse</remote-id>
-</upstream>
-</pkgmetadata>