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| author |   Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> | 2011-05-11 10:58:07 +0200 |
|---|---|---|
| committer | Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> | 2011-05-11 10:58:07 +0200 |
| commit | 46b6d2ba846a0e8ea47e0de6da3946d673aa7c79 (patch) | |
| tree | d6492f2b3e1bbd81bb69b1dda44e96fabd7211c8 /sci-biology/gbrowse/files | |
| parent | sci-mathematics/gambit: deleted from old category sci-misc (diff) | |
| download | sci-46b6d2ba846a0e8ea47e0de6da3946d673aa7c79.tar.gz sci-46b6d2ba846a0e8ea47e0de6da3946d673aa7c79.tar.bz2 sci-46b6d2ba846a0e8ea47e0de6da3946d673aa7c79.zip | |
sci-biology/gbrowse-2.26: fixed sanbox violation but webap-config bug pops up afterwards (happens later during install)
(Portage version: 2.1.9.43/git/Linux i686, unsigned Manifest commit)
Diffstat (limited to 'sci-biology/gbrowse/files')
| -rw-r--r-- | sci-biology/gbrowse/files/GBrowseInstall.pm-2.26.patch (renamed from sci-biology/gbrowse/files/GBrowseInstall.pm.patch) | 12 | ||||
| -rw-r--r-- | sci-biology/gbrowse/files/GBrowseInstall.pm-2.33.patch | 32 | ||||
| -rw-r--r-- | sci-biology/gbrowse/files/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm-2.26.patch | 21 |
3 files changed, 59 insertions, 6 deletions
diff --git a/sci-biology/gbrowse/files/GBrowseInstall.pm.patch b/sci-biology/gbrowse/files/GBrowseInstall.pm-2.26.patch index 863930e58..4c17f8d9a 100644 --- a/sci-biology/gbrowse/files/GBrowseInstall.pm.patch +++ b/sci-biology/gbrowse/files/GBrowseInstall.pm-2.26.patch @@ -1,5 +1,5 @@ ---- GBrowse-2.26/install_util/GBrowseInstall.pm.ori 2010-11-27 12:01:58.000000000 +0100 -+++ GBrowse-2.26/install_util/GBrowseInstall.pm 2010-11-27 12:02:15.000000000 +0100 +--- 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); } @@ -11,8 +11,8 @@ my $base = basename($self->install_path->{htdocs}); ---- GBrowse-2.26/install_util/GBrowseInstall.pm.ori 2011-02-14 13:39:46.000000000 +0100 -+++ GBrowse-2.26/install_util/GBrowseInstall.pm 2011-02-14 13:41:50.000000000 +0100 +--- 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 = $1; @@ -51,8 +51,8 @@ # chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave'); # $self->fix_selinux; ---- GBrowse-2.26/install_util/GBrowseInstall.pm.ori 2011-02-14 13:50:41.000000000 +0100 -+++ GBrowse-2.26/install_util/GBrowseInstall.pm 2011-02-14 13:51:46.000000000 +0100 +--- install_util/GBrowseInstall.pm.ori 2011-02-14 13:50:41.000000000 +0100 ++++ install_util/GBrowseInstall.pm 2011-02-14 13:51:46.000000000 +0100 @@ -470,11 +470,11 @@ my @inc = map{"-I$_"} split ':',$self->added_to_INC; system $perl,@inc,$metadb_script; diff --git a/sci-biology/gbrowse/files/GBrowseInstall.pm-2.33.patch b/sci-biology/gbrowse/files/GBrowseInstall.pm-2.33.patch new file mode 100644 index 000000000..e91fe1634 --- /dev/null +++ b/sci-biology/gbrowse/files/GBrowseInstall.pm-2.33.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/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 new file mode 100644 index 000000000..0dde70406 --- /dev/null +++ b/sci-biology/gbrowse/files/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm-2.26.patch @@ -0,0 +1,21 @@ +--- 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' |