Permalink
Browse files

fix broken configuration process

  • Loading branch information...
1 parent a28bf0b commit e79f1437b1e2ac2f8875787ce60677eda490e306 @lstein lstein committed Aug 25, 2011
View
@@ -4,7 +4,7 @@
"Lincoln Stein <lincoln.stein@gmail.com>"
],
"dynamic_config" : 0,
- "generated_by" : "Module::Build version 0.38, CPAN::Meta::Converter version 2.110930",
+ "generated_by" : "Module::Build version 0.38, CPAN::Meta::Converter version 2.112150",
"license" : [
"perl_5"
],
@@ -22,7 +22,7 @@
},
"configure" : {
"requires" : {
- "Module::Build" : "0.38"
+ "Module::Build" : "0.36"
}
},
"runtime" : {
@@ -47,7 +47,7 @@
"Term::ReadKey" : 0
},
"requires" : {
- "Bio::Graphics" : "2.09",
+ "Bio::Graphics" : "2.24",
"Bio::Root::Version" : "1.0069",
"CGI::Session" : "4.02",
"Digest::MD5" : 0,
@@ -59,6 +59,7 @@
"LWP" : 0,
"Statistics::Descriptive" : 0,
"Storable" : 0,
+ "Text::ParseWords" : "3.27",
"perl" : "5.008"
}
}
@@ -102,7 +103,7 @@
},
"Bio::Graphics::Browser2" : {
"file" : "lib/Bio/Graphics/Browser2.pm",
- "version" : "2.33"
+ "version" : "2.39"
},
"Bio::Graphics::Browser2::Action" : {
"file" : "lib/Bio/Graphics/Browser2/Action.pm",
@@ -256,6 +257,10 @@
"file" : "lib/Bio/Graphics/Browser2/Render/Slave/Status.pm",
"version" : 0
},
+ "Bio::Graphics::Browser2::Render::TrackConfig" : {
+ "file" : "lib/Bio/Graphics/Browser2/Render/TrackConfig.pm",
+ "version" : 0
+ },
"Bio::Graphics::Browser2::RenderPanels" : {
"file" : "lib/Bio/Graphics/Browser2/RenderPanels.pm",
"version" : 0
@@ -367,5 +372,5 @@
"http://dev.perl.org/licenses/"
]
},
- "version" : "2.33"
+ "version" : "2.39"
}
View
@@ -1,55 +0,0 @@
-I suggest you test GBrowse from its development directory rather than
-doing "make install". The reason for this is that the installation
-scripts haven't been updated in a while, and probably won't work!
-
-Assuming that you have unpacked GBrowse into
-/home/aelnaiem/GBrowse, here is a template Apache
-configuration devoted to GBrowse testing:
-
- Listen 8080
- NameVirtualHost *:8080
- <VirtualHost *:8080>
- ServerAdmin webmaster@localhost
-
- DocumentRoot /home/aelnaiem/GBrowse/htdocs/
- <Directory />
- Options FollowSymLinks
- AllowOverride None
- </Directory>
-
- <Directory /home/aelnaiem/GBrowse/htdocs/>
- Options Indexes FollowSymLinks MultiViews
- AllowOverride None
- Order allow,deny
- allow from all
- </Directory>
-
- ScriptAlias /cgi-bin/ /home/aelnaiem/GBrowse/cgi-bin/
- <Directory "/home/aelnaiem/GBrowse/cgi-bin/">
- SetEnv GBROWSE_MASTER GBrowse.conf
- SetEnv GBROWSE_CONF /home/aelnaiem/GBrowse/conf
- SetEnv GBROWSE_DOCS /home/aelnaiem/GBrowse/htdocs
- SetEnv GBROWSE_ROOT /
- AllowOverride None
- Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
- Order allow,deny
- Allow from all
- </Directory>
-
- ErrorLog /var/log/apache2/error.log
- LogLevel warn
- CustomLog /var/log/apache2/access.log combined
- ServerSignature On
- </VirtualHost>
-
-This will create a virtual host listening on port 8080.
-
-Please make note of all occurrences of
-/home/fred/src/Generic-Genome-Browser. This will need to be replaced
-with the path in which you unpacked GBrowse. Also be sure to replace
-/var/log/apache2/ with the location of your error logs and
-/home/fred/src/bioperl-live with the location of bioperl-live, if you
-have not installed it.
-
-Lincoln Stein
-August 2008
View
@@ -3,13 +3,13 @@
# as the various constants formerly scattered amongst scripts and libraries
[GENERAL]
-config_base = /home/aelnaiem/GBrowse/conf # overridden by environment variable GBROWSE_CONF
-htdocs_base = /home/aelnaiem/GBrowse/htdocs
+config_base = $CONF # overridden by environment variable GBROWSE_CONF
+htdocs_base = $HTDOCS
url_base = /gbrowse2
-tmp_base = /tmp/gbrowse2
-persistent_base = /var/lib/gbrowse2
-userdata_base = /var/lib/gbrowse2/userdata
-db_base = /var/lib/gbrowse2/databases
+tmp_base = $TMP
+persistent_base = $PERSISTENT
+userdata_base = $PERSISTENT/userdata
+db_base = $PERSISTENT/databases
# These paths are relative to the url base
buttons = images/buttons
View
No changes.
View
No changes.
View
No changes.
View
No changes.
View
0 contrib/SynView/MAL11/MAL11.gff3 100755 → 100644
No changes.
View
0 contrib/blast2gff.pl 100644 → 100755
No changes.
View
0 debian/postinst 100755 → 100644
No changes.
View
0 debian/prerm 100755 → 100644
No changes.
View
0 debian/rules 100755 → 100644
No changes.
@@ -16,6 +16,9 @@ use File::Compare 'compare';
use File::Copy 'copy';
use GBrowseGuessDirectories;
+use overload '""' => 'asString',
+ fallback => 1;
+
use constant REGISTRATION_SERVER => 'http://modencode.oicr.on.ca/cgi-bin/gbrowse_registration';
my @OK_PROPS = (conf => 'Directory for GBrowse\'s config and support files?',
@@ -964,6 +967,8 @@ END
return $result;
}
+sub asString { return 'GBrowse installer' }
+
1;
__END__
View
0 install_util/cgi_install.pl 100644 → 100755
No changes.
View
0 install_util/conf_install.pl 100644 → 100755
No changes.
View
0 install_util/htdocs_install.pl 100644 → 100755
No changes.
View
0 install_util/make_clean_add.pl 100644 → 100755
No changes.
View
No changes.
View
No changes.
@@ -114,7 +114,7 @@ END
TIMESTAMP => 'Snapshot Timestamp [GMT]',
- SNAPSHOT_SELECT => 'Saved Snapshots',
+ SNAPSHOT_SELECT => 'Snapshots',
SELECT_TRACKS => 'Select Tracks',

0 comments on commit e79f143

Please sign in to comment.