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

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1 parent 3c844ce commit f48b02845fec16b26e8ac4d432e0355f8c88d2cc Sheldon McKay committed Apr 29, 2014
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1 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
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4 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
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2 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
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2 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
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3 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};

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