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

["Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>]

commit:     fa7a65b1a985d0cd4c830b8cac8e63ce2e576c28
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Jul 30 14:45:25 2011 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Jul 30 14:45:25 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=fa7a65b1

sci-biology/gbrowse: added support for --destdir, patch sent to upstream

(Portage version: 2.1.10.7/git/Linux i686, unsigned Manifest commit)

---
 sci-biology/gbrowse/ChangeLog           |    8 +++
 sci-biology/gbrowse/files/destdir.patch |   92 +++++++++++++++++++++++++++++++
 sci-biology/gbrowse/gbrowse-2.39.ebuild |    3 +-
 3 files changed, 102 insertions(+), 1 deletions(-)

diff --git a/sci-biology/gbrowse/ChangeLog b/sci-biology/gbrowse/ChangeLog
index b8780b1..5c2bd3e 100644
--- a/sci-biology/gbrowse/ChangeLog
+++ b/sci-biology/gbrowse/ChangeLog
@@ -3,6 +3,14 @@
 # $Header: /var/cvsroot/gentoo-x86/sci-biology/generic-genome-browser/ChangeLog,v 1.10 2007/07/29 17:07:38 phreak Exp $
 
   30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  gbrowse-2.39.ebuild, +files/destdir.patch:
+  added support for --destdir, patch sent to upstream gbrowse-2.39.ebuild
+
+  30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  gbrowse-2.39.ebuild, +files/destdir.patch:
+  added support for --destdir, patch sent to upstream
+
+  30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   -gbrowse-2.38.ebuild, -files/GBrowseInstall.pm-2.38.patch,
   +gbrowse-2.39.ebuild, +files/GBrowseInstall.pm-2.39.patch:
   version bump but still need to rewrite upstream's install procedure to

diff --git a/sci-biology/gbrowse/files/destdir.patch b/sci-biology/gbrowse/files/destdir.patch
new file mode 100644
index 0000000..655158c
--- /dev/null
+++ b/sci-biology/gbrowse/files/destdir.patch
@@ -0,0 +1,92 @@
+--- install_util/GBrowseInstall.pm.ori	2011-07-30 16:06:18.000000000 +0200
++++ install_util/GBrowseInstall.pm	2011-07-30 16:06:28.000000000 +0200
+@@ -419,6 +419,7 @@
+ sub ACTION_install {
+     my $self = shift;
+     my $prefix = $self->install_base || $self->prefix || '';
++    my $destdir = $self->destdir || '';
+     GBrowseGuessDirectories->prefix($prefix);
+ 
+     $self->depends_on('config_data');
+@@ -445,7 +446,7 @@
+ 
+     # fix some directories so that www user can write into them
+     my $tmp = $self->config_data('tmp') || GBrowseGuessDirectories->tmp;
+-    mkpath($tmp);
++    mkpath($destdir.$tmp);
+     my ($uid,$gid) = (getpwnam($user))[2,3];
+ 
+     # taint check issues
+@@ -454,29 +455,29 @@
+     $gid =~ /^(\d+)$/;
+     $gid = $1;
+     
+-    unless (chown $uid,$gid,$tmp) {
++    unless (chown $uid,$gid,$destdir.$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 $uid,-1,$destdir.$htdocs;
+     {
+ 	local $> = $uid;
+ 	symlink($images,$htdocs_i);  # so symlinkifowner match works!
+     }
+-    chown $>,-1,$self->install_path->{htdocs};
++    chown $>,-1,$destdir.$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([$destdir.$sessions,$destdir.$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($destdir.File::Spec->catfile($databases,'').'*')) {
++	$self->ownership_warning($destdir.$databases,$user);
+     }
+ 
+     # chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave');
+@@ -490,7 +491,7 @@
+     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 'sudo','chown','-R',"$uid.$gid",$destdir.$sessions,$destdir.$userdata;
+ 
+ #    if (Module::Build->y_n(
+ #	    "It is recommended that you restart Apache. Shall I try this for you?",'y'
+@@ -600,6 +601,7 @@
+     my $self = shift;
+ 
+     my $prefix = $self->install_base || $self->prefix || '';
++    my $destdir = $self->destdir || '';
+     GBrowseGuessDirectories->prefix($prefix);
+     my $install_path = GBrowseGuessDirectories->etc;
+ 
+@@ -647,7 +649,7 @@
+ 	if ($self->config_data('installconf') =~ /^[yY]/ && !-e "${includes}/$file") {
+ 	    warn "Creating include file for Apache config: $target\n";
+ 	    my $dir = dirname($target);
+-	    mkpath([$dir]);
++	    mkpath([$destdir.$dir]);
+ 	    if (my $f = IO::File->new("blib${includes}/$file",'>')) {
+ 		$f->print($self->apache_conf);
+ 		$f->close;
+@@ -935,8 +937,9 @@
+ sub ownership_warning {
+     my $self = shift;
+     my ($path,$owner) = @_;
++    my $destdir = $self->destdir || '';
+     warn "*** WARNING: Using sudo to change ownership of $path to '$owner'. You may be prompted for your login password ***\n";
+-    system "sudo chown -R $owner $path";
++    system "sudo chown -R $owner $destdir.$path";
+ }
+ 
+ sub cgiurl {

diff --git a/sci-biology/gbrowse/gbrowse-2.39.ebuild b/sci-biology/gbrowse/gbrowse-2.39.ebuild
index 426ee4b..0acd25a 100644
--- a/sci-biology/gbrowse/gbrowse-2.39.ebuild
+++ b/sci-biology/gbrowse/gbrowse-2.39.ebuild
@@ -89,7 +89,8 @@ RDEPEND="${DEPEND}
 src_prepare() {
 	sed -i 's/return unless -t STDIN/return/' install_util/GBrowseInstall.pm || die
 	sed -i 's/process_/bp_process_/g' INSTALL || die
-	epatch "${FILESDIR}"/GBrowseInstall.pm-"${PV}".patch || die "Failed to patch"
+	epatch "${FILESDIR}"/GBrowseInstall.pm-"${PV}".patch || die "Failed to apply GBrowseInstall.pm-"${PV}".patch"
+	epatch "${FILESDIR}"/destdir.patch || die "Failed to apply destdir.patch "
 }
 
 src_configure() {