GBrowse Persistent Variables

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GBrowse uses a few persistent variables to store data for a user. The following is an explanation of the structure of the commonly-used ones:


$session is a blessed Browser2::Session object containing information regarding the current user's session. It contains the following key->value pairs:

    • pid [number] - The process ID number of the session.
    • lockdir [string] - The directory path holding the lock information.
    • locktype [string] - The type of lock used.
    • lockobj [hash] - The blessed File::NFSLock object, containing details of the session.
    • session [hash] - A blessed CGI::Session object containing the session. The only data we need to worry about is in:
      • _DATA [hash] - Holds all the stored session data, with the data source name as the key.
        • [hash] -
          • plugins [hash] - A collection of data stored by individual plugins, collected with the plugin name as a key.
          • page_settings [hash] - The page settings, as stored in $state


$state is a large hash containing information regarding the current configured state of the browser (hence the name). It contains the following key->value pairs:

    • width [string] - The width of the final image, in pixels, as set on the preferences tab.
    • source [string] - The current data source name.
    • ks [string] - ?
    • tracks [array] - An array of the labels of all the tracks for the
    • userid [string] - The currently-logged-in user's ID, corresponding to the main GBrowse user database.
    • uploadid [string] - The currently-logged-in user's uploads ID, corresponding to the folder containing their uploaded files.
    • seg_max [number] - The upper bound of the region currently being viewed; the right side of the image, unless flipped.
    • seg_min [number] - The lower bound of the region currently being viewed; the left side of the image, unless flipped.
    • flip [boolean] - True if the genome view has been flipped horizontally from the default left-to-right method.
    • show_tooltips [boolean] - Whether or not to show the helper tooltips in the main browser.
    • valid_region [boolean] - Whether the region requested is valid, or not. If not, the karotype is shown.
    • uploads [hash] - Contains all uploaded (not imported) files as keys, the values are arrays containing: ["uploaded file's name", "?"]
    • track_collapsed [hash] - ? "between"
    • region_size [number] - The size (in base pairs) of the region being viewed.
    • max segment [number] - ? 5000000
    • head [boolean] - ? 1
    • grid [boolean] - Whether or not to display the grid behind the rendered images
    • features [hash] - All the features available; the feature name is the key and the value is another hash containing 3 flags:
      • visible [boolean] - Whether or not the feature is visible in the browser display.
      • options [boolean] - ? 0
      • limit [boolean] - ? 0
    • version [number] - ? 100
    • stop [number] - ? 203999
    • ref [string] - The named region being displayed (?)
    • name [string] - The displayed name of the region (as seen in the "Landmark or Region" input field), "chrI:98000..203999" for example.
    • v [number] - ? 2
    • subtracks [hash] - ? {}
    • ins [boolean] - ? 1
    • stp [boolean] - ? 1
    • sk [string] - ? "sorted"
    • section_visible [hash] - A hash containing each section as a key and a boolean flag indicating whether a section is visible (true) or not (false).
    • cache [boolean] - Whether or not to cache the rendered images.
    • start [number] - 98000'

Querying the State Variable

To query the value of your state variables, copy and paste the Named Subroutines below to a file called init_code.conf.

    my $t = -1;
    my $toString;
    sub queryVariables {
        my @arg  = @_;
        for(my $i=0; $i<@arg; $i++) {
            if( ref($arg[$i]) eq "HASH" ) {
                my %hash = %{$arg[$i]};
                foreach my $key ( keys %hash ) {
                    if( ref(\$hash{$key}) eq "SCALAR" ) {
                        $toString .= "\t"x$t."HASH key: $key\tvalue: $hash{$key}\n";
                    } else {
                        $toString .= "\t"x$t."HASH key: $key\tvalue: ".ref($hash{$key})."\n";
                        queryVariables( $hash{$key} );
            } elsif( ref($arg[$i]) eq "ARRAY" ) {
                my @array = @{$arg[$i]};
                for(my $j=0; $j<@array; $j++){
                    if( ref(\$array[$j]) eq "SCALAR" ) {
                        $toString .= "\t"x$t."ARRAY element[$j]: $array[$j]\n";
                    } else {
                        $toString .= "\t"x$t."ARRAY element[$j]: ".ref($array[$j])."\n";
                        queryVariables( @array );
        return $toString;
    sub queryStateVariables {
        my $stateVariables = queryVariables( @_ );
        $stateVariables = "<pre>\n".$stateVariables."</pre>n";
        return $stateVariables;

In your GBrowse.conf file, use the include directive to import the named subroutines, by including the init_code.conf file in the [GENERAL] section of the configuration file. Add a reference to the named subroutine queryStateVariables, assigning the return value to one of the html variables.

Displaying the values of the $state variable
#include "path/to/init_code.conf"

# Various places where you can insert your own HTML -- see configuration docs
html1 =
html2 =
html3 = \&queryStateVariables
html4 =
html5 =
html6 =

After refreshing GBrowse, you should see the values of the state hash and the values of any other hashes or arrays that have been referenced.

Querying the state variable should be helpful in creating other subroutines to do more specific things. After you are finished querying the contents of the state variable, you can remove the reference to the subroutine so that the main GBrowse page appears normally.


$globals is essentially an object containing the GBrowse.conf file.