A few tweaks to make GBrowse_syn install work out of the box

GMOD · Apr 29, 2014 · f48b028 · f48b028
1 parent 3c844ce
commit f48b028
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Showing 5 changed files with 8 additions and 4 deletions.
diff --git a/MANIFEST b/MANIFEST
@@ -346,6 +346,7 @@ htdocs/images/help/overview+detail.png
 htdocs/images/help/overview.gif
 htdocs/images/help/remote.png
 htdocs/images/help/search+settings.gif
+htdocs/images/help/sugarcane_sorghum_synteny.png
 htdocs/images/help/track+settings.gif
 htdocs/images/help/upload+edit.gif
 htdocs/images/help/upload+remote.gif

diff --git a/conf/synteny/oryza.synconf.disabled.conf b/conf/synteny/oryza.synconf.disabled.conf
@@ -2,7 +2,7 @@
 description =  BLASTZ alignments for Oryza sativa 
 
 # The synteny database
-join        = dbi:mysql:database=rice_synteny;host=localhost
+join        = dbi:mysql:database=rice_synteny;host=localhost;user='www-data'
 
 # This option maps the relationship between the species data sources, names and descriptions
 # The value for "name" (the first column) is the symbolic name that gbrowse_syn users to identify each species.
@@ -15,7 +15,7 @@ join        = dbi:mysql:database=rice_synteny;host=localhost
 source_map =      rice          rice_synteny          "Domesic Rice (O. sativa)"
                   wild_rice     wild_rice_synteny     "Wild Rice"
 
-tmpimages     = /tmp/gbrowse_syn
+tmpimages     = /gbrowse2/tmp/gbrowse_syn
 imagewidth    = 800
 stylesheet    = /gbrowse2/css/gbrowse_transparent.css
 cache time    = 1

diff --git a/conf/synteny/rice_synteny.conf b/conf/synteny/rice_synteny.conf
@@ -6,7 +6,7 @@ db_args       = -adaptor memory
 
 
 # Web site configuration info
-tmpimages   = /tmp/gbrowse_syn
+tmpimages   = /gbrowse2/tmp/gbrowse_syn
 
 [EG]
 feature      = gene:ensembl

diff --git a/conf/synteny/wild_rice_synteny.conf b/conf/synteny/wild_rice_synteny.conf
@@ -6,7 +6,7 @@ db_args       = -adaptor memory
 
 
 # Web site configuration info
-tmpimages   = /tmp/gbrowse_syn
+tmpimages   = /gbrowse2/tmp/gbrowse_syn
 
 ################## TRACK CONFIGURATION ####################
 # the remainder of the sections configure individual tracks

diff --git a/install_util/GBrowseInstall.pm b/install_util/GBrowseInstall.pm
@@ -477,6 +477,7 @@ sub ACTION_install {
     # fix some directories so that www user can write into them
     my $tmp = $self->config_data('tmp') || GBrowseGuessDirectories->tmp;
     mkpath($tmp);
+
     my ($uid,$gid) = (getpwnam($user))[2,3];
 
     # taint check issues
@@ -491,11 +492,13 @@ sub ACTION_install {
 
     my $htdocs_i = File::Spec->catfile($self->install_path->{htdocs},'i');
     my $images   = File::Spec->catfile($tmp,'images');
+    my $gbs_tmp  = File::Spec->catfile($self->install_path->{htdocs},'tmp');
     my $htdocs = $self->install_path->{htdocs};
     chown $uid,-1,$htdocs;
     {
 	local $> = $uid;
 	symlink($images,$htdocs_i);  # so symlinkifowner match works!
+	symlink($tmp,$gbs_tmp);
     }
     chown $>,-1,$self->install_path->{htdocs};