INSTALL

Generic Genome Browser Installation
    GBrowse is distributed as binary packages for Windows and Macintosh OS
    X, and as source code for Unix systems. For binary installations, please
    see the online instructions located at

    <http://www.gmod.org/wiki/index.php/GBrowse#Installation>

    The remainder of this documentation contains instructions are for a
    source code (manual) build.

Source Code (Manual) Build
    GBrowse runs on top of several software packages. These must be
    installed and configured before you can run GBrowse. Most preconfigured
    Linux systems will have some of these packages installed already.

    A) MySQL -- <http://www.mysql.com>
        The MySQL database is a fast open source relational database that is
        widely used for web applications. For small projects (a few
        thousands of annotated features), you can skip installing MySQL and
        use an in-memory database instead.

    B) Apache Web Server -- <http://www.apache.org>
        The Apache web server is the industry standard open source web
        server for Unix and Windows systems.

    C) Perl 5.005 -- <http://www.cpan.org>
        The Perl language is widely used for web applications. Version 5.6
        is preferred, but 5.00503 or higher will work.

    D) Standard Perl modules -- <http://www.cpan.org>
        The following Perl modules must be installed for GBrowse to work.
        They can be found on the Comprehensive Perl Archive Network (CPAN):

           CGI                  (2.56 or higher)
           GD                   (2.07 or higher)
           CGI::Session         (4.03 or higher)
           DBI                  (any version)
           DBD::mysql           (any version)
           Digest::MD5          (any version)
           Text::Shellwords     (any version)
           Class::Base          (any version)

    E) BioPerl version 1.6 or higher -- <http://www.bioperl.org>
        Or 'bioperl-live'.

    F) Bio::Graphics 1.97 or higher
        Bio::Graphics used to be part of BioPerl but has been broken out as
        a separate package that can be installed from CPAN.

    Optional modules:

    F) XML::Parser, XML::Writer, XML::Twig, XML::DOM
        If these modules are present, the "Sequence Dumper" plugin will be
        able to produce GAME and BSML output. They can be downloaded from
        CPAN.

    G) LWP
        To load remote 3d party annotations. Available from CPAN.

    H) Bio::Das
        To display remote annotations using the Distributed Annotation
        System. The current version is available at
        http://www.biodas.org/download/Bio::Das/Bio-Das-0.92.tar.gz

    I) MOBY
        Needed by gbrowse_moby to fetch and display data from MOBY
        providers. Available from biomoby.org; obtain via anonymous cvs
        until it is released. Directions are at
        http://www.biomoby.org/GettingTheCode.html.

    J) GD::SVG
        To save images as publication-quality editable images in Scalar
        Vector Graphics format. Available from CPAN.

    K) Bio::SCF File::Temp io-lib(v1.7+)
        Needed by the trace glyph which can parse SCF files and display the
        trace graph. The io-lib library can be downlowded from
        https://sourceforge.net/project/showfiles.php?group_id=100316&packag
        e_id=108243 which is part of the Staden Package
        https://sourceforge.net/projects/staden/.

    Once the prerequisites are installed, download the most recent version
    of the Generic-Genome-Browser source code from:

       L<http://prdownloads.sourceforge.net/gmod>

    This will give you a .tar.gz file, which must be uncompressed and
    unpacked. Then run the following commands (in brief):

       perl Makefile.PL
       make
       make test (optional)
       make install UNINST=1

    This will install the software in the default location under
    /usr/local/apache. See "Details" to change this, or to install gbrowse
    into your home directory. The 'UNINST=1' will insure that older versions
    of perl modules being installed will be removed to help prevent
    conflicts.

    To further configure GBrowse, see CONFIGURE_HOWTO. To run GBrowse on top
    of Oracle and PostgreSQL databases see ORACLE_AND_POSTGRESQL. To run on
    top of a BioSQL database, see BIOSQL_ADAPTER_HOWTO.

    Details:

    The browser consists of a CGI script named "gbrowse", a Perl module that
    handles some of the gory details, a small number of static image files,
    and a configuration directory that contains configuration files for each
    data source. The correct locations of these CGI script, configuration
    directory and static files depend on how Apache was installed on your
    system, which varies from operating system to operating system, and are
    controlled by the following installation options:

       CGI script:      /usr/local/apache/cgi-bin/gbrowse
       Static images:   /usr/local/apache/htdocs/gbrowse
       Config files:    /usr/local/apache/conf/gbrowse.conf
       The module:      -standard site-specific Perl library location-

    You can change change the location of the installation by passing
    Makefile.PL one or more NAME=VALUE pairs, like so:

      perl Makefile.PL CONF=/etc HTDOCS=/home/html

    This will cause the configuration files to be installed in
    /etc/gbrowse.conf and the static files to be installed in
    /home/html/gbrowse.

    Fortunately, this isn't usually necessary. The Makefile.PL script
    attempts to guess the appropriate directory locations for your system,
    but sometimes you will have to specify them manually. For example, if
    you are on an unusual system, where the Apache installation uses
    /opt/www/html for HTML files, /opt/run/cgi-bin for CGI scripts, and
    /etc/httpd/conf for the configuration files, you should specify the
    following configuration: perl Makefile.PL HTDOCS=/opt/www/html \
    CONF=/etc/httpd/conf \ CGIBIN=/opt/run/cgi-bin

    As a convenience, you can use the configuration option APACHE, in which
    case the static and CGI files will be placed into APACHE/conf,
    APACHE/htdocs and APACHE/cgi-bin respectively, where APACHE is the
    location you specified on the command line:

      perl Makefile.PL APACHE=/home/www

    Note that the configuration files are always placed in a subdirectory
    named gbrowse.conf. You cannot change this. Similarly, the static files
    are placed in a directory named gbrowse. The install script will detect
    if there are already configuration files in the selected directory and
    not overwrite them if so. The same applies to the cascading stylesheet
    file (gbrowse.css) located in the gbrowse subdirectory. However, neither
    the GIF files in the "buttons" subdirectory nor the plugin modules in
    the gbrowse.conf/plugins directory are checked before overwriting them,
    so be careful to copy the new copies somewhere safe if you have modified
    them.

    The DO_XS flag, if true (perl Makefile.PL DO_XS=1), will compile a small
    C subroutine for nucleotide alignments. This will vastly improve the
    performance of the gbrowse_details script when displaying alignments. To
    use this feature, you will need a C compiler.

    You can always manually move the files around after install. See
    CONFIGURE_HOWTO for details.

    When installing the static files, the install script also creates an
    empty directory named "tmp". This directory is set to be world writable
    so that the GBrowse server can use it to manage temporary image files
    that it creates on the fly. If you would prefer not to have a world
    writable directory on your system, simply change the ownership and
    permissions to allow the web server account to write into it. The
    directory is located in HTDOCS/gbrowse/tmp by default.

    The first time you run Makefile.PL, a file named GGB.def will be created
    your file path settings. When Makefile.PL is run again, it will ask you
    whether you wish to reuse the settings stored in the file.

  4. INSTALLING INTO YOUR HOME DIRECTORY
    Read this section only if you are on a Unix system and do not have root
    privileges. You will need to configure Apache to run out of your home
    directory. One way to do this is to install Apache from source code and
    to specify your home directory when you first configure it:

       % cd apache_x.xx.xx
       % ./configure --prefix=$HOME/apache
       % make
       % make install

    This will place Apache into your home directory under ~/apache. You
    should then edit ~/apache/conf/httpd.conf and replace the directive:

      Listen 80

    with

      Listen 8000

    so that Apache will listen for connections to the unprivileged port 8000
    rather than the usual port 80. If you also see a "Port 80" directive,
    change it to read "Port 8000." You will now be able to talk to Apache
    using URLs like http://your.host.edu:8000/.

    You may not need to install Apache from scratch if your Unix
    distribution already has Apache installed. What you will do is to create
    an Apache directory tree in your home directory and then start Apache
    using command-line arguments that tell it to start up from the home
    directory rather than its default system-wide directory.

    Create an Apache directory and its subdirectories using the following
    series of commands:

      % cd ~
      % mkdir apache
      % mkdir apache/conf
      % mkdir apache/logs
      % mkdir apache/htdocs
      % mkdir apache/cgi-bin

    Now copy the system-wide httpd.conf into ~/apache/conf. You may need to
    search around a bit to find out where the system-wide httpd.conf lives
    (try running the command "locate httpd.conf"):

      % cp /etc/httpd/conf/httpd.conf ~/apache/conf

    Now open up ~/apache/conf/httpd.conf with a text editor and add the
    following four directives, replacing $HOME with the full path to your
    home directory (for example "/home/fred"):

      Listen       8000
      ServerRoot   $HOME/apache
      DocumentRoot $HOME/apache/htdocs
      SetEnv       PERL5LIB $HOME/lib

    You should search the httpd.conf file for older versions of these
    directives, and delete them if they are there. If you see a Port
    directive, change it to read "Port 8000".

    Somewhere in httpd.conf there will be a ScriptAlias directives, as well
    as a <Directory> section that refers to "cgi-bin". Delete the
    ScriptAlias directive and the entire <Directory> section through to the
    </Directory> line. Replace both these sections with the following:

     ScriptAlias /cgi-bin/ "cgi-bin/"

     <Location "/cgi-bin">
        AllowOverride None
        Options None
        Order allow,deny
        Allow from all
     </Location>

    You can now start Apache from the command line using the "apachectl"
    script:

     % /usr/sbin/apachectl -d ~/apache -k start

    If Apache starts successfully, then this command will return silently.
    Otherwise, it will print an error message. More error messages may be
    found in ~/apache/logs/error_log.

    To confirm that Apache is running from your home directory, create a
    file named index.html and copy it into ~/apache/htdocs. You should then
    be able to open a browser, connect to http://localhost:8000/, and see
    the index.html file that you just created.

    Now you can build and install gbrowse with the following incantation:

     % cd Generic-Genome-Browser-X.XX
     % perl Makefile.PL APACHE=~/apache LIB=~/lib BIN=~/bin NONROOT=1
     % make
     % make install

    When you are prompted to load gbrowse using http://localhost/gbrowse,
    use http://localhost:8000/gbrowse instead.

  5. TRY THE BROWSER OUT
    The installation procedure will create a small in-memory database of
    yeast chromosome 1 for you to play with. To try the browser out, use
    your favorite browser to open:

      http://localhost/cgi-bin/gbrowse

    Try searching for "I" (the name of the first chromosome of yeast), or a
    gene such as NUT21 or TCF3. Then try searching for "membrane
    trafficking."

    For your interest, the feature and DNA files for this database is
    located in the Apache document root at gbrowse/databases/yeast_chr1. The
    configuration file is in the web server configuration directory under
    gbrowse.conf/yeast1.conf.

    More configuration information and a short tutorial are located at:

       http://localhost/gbrowse

  6. POPULATING THE DATABASE (MySQL)
    This step takes you through populating the database with the full yeast
    genome. You can skip this step if you use the in-memory database for
    small projects (see section 6).

    Remember as well that there are other datbase possibilities. For example
    you could also use BioSQL (Mysql, Postgres, Oracle) or Chado (Postgres).
    See ORACLE_AND_POSTGRESQL for more.

    This example uses Mysql as it is relatively easy to set up.

    Synopsis:

      mysql -uroot -p password -e 'create database yeast'
      mysql -uroot -p password -e 'grant all privileges on yeast.* to me@localhost'
      mysql -uroot -p password -e 'grant file on *.* to me@localhost'
      mysql -uroot -p password -e 'grant select on yeast.* to nobody@localhost'

      bp_bulk_load_gff.pl -d yeast sample_data/yeast_data.gff

    Details:

     Note: This section refers to the user account under which Apache runs
     as "nobody" because that is the most common case. However, many
     systems use a different user account. Mac OSX uses "www", Fedora Core
     uses "apache" and Ubuntu uses "www-data." In the instructions that
     follow, replace 'nobody' with the appropriate Apache account name.

    You will need an installation of MySQL for this section. Using the mysql
    command line, create a database (called "yeast" in the synopsis above),
    and ensure that you have update and file privileges on it. The example
    above assumes that you have a username of "me" and that you will allow
    updates from the local machine only. It also gives all privileges to
    "me". You may be comfortable with a more restricted set of privileges,
    but be sure to provide at least SELECT, UPDATE and INSERT privileges.
    You will need to provide the administrator's name and correct password
    for these commands to succeed.

    In addition, grant the "nobody" user the SELECT privilege. The web
    server usually runs as nobody, and must be able to make queries on the
    database. Modify this as needed if the web server runs under a different
    account.

    The next step is to load the database with data. This is accomplished by
    loading the database from a tab-delimited file containing the genomic
    annotations in GFF format. The Bioperl distribution comes with three
    tools for loading Bio::DB::GFF databases:

    1 bp_load_gff.pl
        This will incrementally load a database, optionally initializing it
        if it does not already exist. This script will work correctly even
        if the MySQL server is located on another host.

    2 bp_bulk_load_gff.pl
        This Perl script will initialize a new Bio::DB::GFF database with a
        fresh schema, deleting anything that was there before. It will then
        load the file. Only suitable for use the very first time you create
        a database, or when you want to start from scratch! The bulk loader
        is as much as 10x faster than bp_load_gff.pl, but does not work in
        the situation in which the MySQL database is running on a remote
        host.

    3 bp_fast_load_gff.pl
        This will incrementally load a database. On UNIX systems, it will
        activate a fast loader that makes the speed almost the same as the
        bulk loader. Be careful, though, because this is an experimental
        piece of software.

    You will find these scripts in the Bioperl distribution, in the
    subdirectory scripts/Bio-DB-GFF. If you requested that Bioperl scripts
    be installed during installation, they will also be found in your
    command path.

    For testing purposes, this distribution includes a GFF file with yeast
    genome annotations. The file can be found in the test_data subdirectory.
    If the load is successful, you should see a message indicating that
    13298 features were successfully loaded.

    Provided that the yeast load was successful, you may now run "make
    test". This invokes a small test script that tests that the database is
    accessible by the "nobody" user and that the basic feature retrieval
    functions are working.

    You may also wish to load the yeast DNA, so that you can test the
    three-frame translation and GC content features of the browser. Because
    of its size, the file containing the complete yeast genome is
    distributed separately and can be downloaded from:

    <http://prdownloads.sourceforge.net/gmod/yeast.fasta.gz?download>

    Load the file with this command:

      bp_load_gff.pl -d yeast -fasta yeast.fasta.gz </dev/null

    You should now be able to browse the yeast genome. Type the following
    URL into your favorite browser:

      http://name.of.your.host/cgi-bin/gbrowse/yeast

    This will display the genome browser instructions and a search field.
    Type in "III" to start searching chromosome III, or search for "glucose"
    to find a bunch of genes that are involved in glucose metabolism.

    *IF YOU GET AN ERROR* examine the Apache server error log (depending on
    how Apache was installed, it may be located in /usr/local/apache/logs/,
    /var/log/httpd/, /var/log/apache, or elsewhere). Usually there will be
    an informative error message in the error log. The most common problem
    is MySQL password or permissions problems.

  7.GFF3 Loading
    An increasing number of model organism databases are distributing genome
    annotation in GFF3 format. An example of this format can be found at SGD
    at
    ftp://genome-ftp.stanford.edu/pub/yeast/chromosomal_feature/saccharomyce
    s_verevisiae.gff. Although these files will load into the standard
    Bio::DB::GFF database, some of the features of GFF3, such as the ability
    to represent multiple alternative splice forms as a single gene, will be
    lost. We suggest instead that you use a Bio::DB::SeqFeature::Store
    database.

    Here is a quick recipe.

    Get a gff3 file (available from SGD, WormBase, FlyBase and many other
    sites) and save it as genome.gff3. Then launch the mysql command-line
    client and run commands similar to these (be sure to replace the example
    user names with correct ones as described earlier).

         mysql -uroot -p password -e 'create database genomegff3'
         mysql -uroot -p password -e 'grant all privileges on genomegff3.* to me@localhost'
         mysql -uroot -p password -e 'grant select on genomegff3.* to nobody@localhost'

         bp_seqfeature_load.pl -d genomegff3 -f -c genome.gff3

    Create a GBrowse config file by copying one of the existing examples,
    and modify the top lines to read like the following:

     db_adaptor    = Bio::DB::SeqFeature::Store
     db_args       = -adaptor DBI::mysql
                     -dsn     dbi:mysql:database=genomegff3
                     -user    nobody

    The database should now be browsable. For more details, see
    Generic-Genome-Browser/README.gff3

  8. LOADING OTHER DATA SETS
    Sample genome feature tables for the major model organisms and human can
    be found at www.gmod.org in the downloads section, but they are
    increasingly out of date. Please go to the individual model organism
    database's web sites to find the GFF or GFF3-format files you need. A
    few notable sites are:

    WormBase (C. elegans)
        <ftp://ftp.wormbase.org/pub/wormbase/genomes/elegans/genome_feature_
        tables/ >

    SGD (S. cerevisiae)
        <ftp://genome-ftp.stanford.edu/pub/yeast/chromosomal_feature/>

    FlyBase (D. melanogaster)
        <ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/
        >

    In addition, the bin/ subdirectory of the GBrowse distribution contains
    a series of scripts to convert annotation files in various formats into
    GFF2 or GFF3 format. For example, the ucsc_genes2gff.pl script will
    convert gene models in Table Browser format files from
    <http://www.genome.ucsc.edu> into GFF3 format.

    load_genbank.pl will download and load sequence annotation files in
    GenBank format from NCBI. The sample configuration file 08.genbank.conf
    (located in contrib/conf_files) is appropriate for data loaded with
    load_genbank.pl.

  9. LOADING DNA
    To display the DNA sequence and to run sequence-dependent glyphs such as
    the three-frame translation, you will need to load the DNA as well as
    the annotations. The DNA must be formatted as a series of one or more
    FASTA-format files in which each entry in the file corresponds to a
    top-level sequence such as a chromosome pseudomolecule. You can then run
    the bp_load_gff.pl or bp_bulk_load_gff.pl script using the -fasta
    argument. For example, if the yeast genome is contained in a FASTA file
    named yeast.fa, you would run the command:

      bp_bulk_load_gff.pl -d yeast -fasta yeast.fa sample/yeast_data.gff

    Alternatively, you may put several FASTA files into a directory, and
    provide the directory name as the argument to -fasta.

    (The yeast DNA is too large to be included in this distribution, but you
    can get a copy of it from <ftp://genome-ftp.stanford.edu/pub/yeast/>)

    Run "bp_bulk_load_gff.pl -h" to see usage instructions.

    Newer versions of GFF (the so-called "GFF2.5" and "GFF3" formats)
    include the DNA at the bottom of the file, following the sequence
    annotations. If you are loading one of these GFF files, the DNA will be
    recognized automatically and loaded by any of the loaders.

  10. CREATING YOUR OWN GENOME DATABASE
    See the file doc/pod/CONFIGURE_HOWTO.pod for information on how to
    create new databases from scratch, add new browser tracks, and how to
    get the browser to dump the DNA from the region currently under display.

  11. MAKING THE BROWSER RUN FASTER
    Three factors are major contributors to the length of time it takes to
    load a gbrowse page:

    1   Loading the Perl interpreter and parsing BioPerl and all the other
        Perl libraries that gbrowse uses.

    2   Query speed on the database

    3   The conversion at the Perl layer of database data into BioPerl
        objects for rendering.

    To improve (1), we recommend that you install the mod_perl module for
    Apache. (<http://perl.apache.org>). By configuring an Apache::Registry
    directory and placing gbrowse inside it (rather than in the default
    cgi-bin directory). The overhead for loading Perl and its libraries are
    eliminated, thereby increasing the performance of the script noticeably.

    Be aware that there is a bad interaction between the Apache::DBI module
    (often used to speed up database accesses) and Bio::DB::GFF. This will
    cause the GFF dumper plugin to fail intermittently. GBrowse does not
    need Apache::DBI to achieve performance increases under mod_perl and it
    is suggested that you disable Apache::DBI. If you cannot do this, then
    you should remove the file GFFDumper.pm from the gbrowse.conf/plugins
    directory.

    Database query performance (2) is also a major factor. If you are using
    MySQL as the backend, you will see dramatic performance increases by
    increasing the amount of memory available to the key buffer, sort
    buffer, table cache and other in-memory data structures. we suggest that
    you replace the default MySQL configuration file (usually stored in
    /etc/my.cnf) with one of the large-memory sample configuration files
    provided in the support-files subdirectory of the MySQL distribution. Of
    course, if you tell MySQL to use more memory than you have, then
    performance will degrade again.

    Finally, there is a slowdown when gbrowse converts the results of
    database SQL queries into renderable biological objects. This becomes
    particularly noticeable when there are lots of multi-segment objects to
    be displayed. You can work around this slowdown by using semantic
    zooming (see CONFIGURE_HOWTO). Otherwise, there's not much that can be
    done about this short of buying a faster machine. The GMOD team is
    working hard to reduce this performance hit.

  12. MAKING THE SERVER RUN SAFER
    Whenever you are running a server-side Web script using information
    provided by a web client, there is a risk that maliciously-formatted
    data provided by the use will trick the server-side script into
    performing some unintentional action, such as modifying a file on the
    server. Perl's "taint" checks are designed to catch places in the code
    where such malicious data could cause harm, and GBrowse has been tested
    extensively with these taint checks activated.

    Because of taint checks' noticeable impact on performance, they have
    been turned off in the distributed version of gbrowse. If you wish to
    reactivate the extra checking (at the expense of a performance hit), go
    to the file "gbrowse" located in the Web scripts directory and edit the
    top line of the file to read:

      #!/usr/bin/perl -w -T

    The -T switch turns on taint checks.

    If you are running GBrowse under mod_perl, add the following line to the
    httpd.conf configuration file:

      PerlTaintCheck  On

    This will affect all mod_perl scripts globally.

  13. THE GBROWSE_IMG SCRIPT
    The gbrowse_img CGI script is a stripped-down version of gbrowse which
    just generates images. It is suitable for incorporating into <img> tags
    in order to make a thumbnail of a region of interest. The thumbnail can
    then be linked to the full-featured gbrowse. Here is an example of how
    this works using the WormBase site:

      <a href="http://www.wormbase.org/db/seq/gbrowse/wormbase?name=mec-3">
        <img src="http://www.wormbase.org/db/seq/gbrowse_img/wormbase?name=mec-3;width=200">
      </a>

    This will generate a 200-pixel inline image of the region. Clicking on
    the image will link to the fully-navigable gbrowse script.

    You can also use gbrowse_img to superimpose temporary features (like
    BLAST hits) on the existing genome features.

    If the script is called without CGI arguments, it will generate usage
    instructions. Select <http://your.host/cgi-bin/gbrowse_img> to see this
    internal documentation.

  14. PLUGINS
    Gbrowse has a plugin architecture which makes it easy for third-party
    developers to expand its functionality. The plugins are Perl .pm files
    located in the directory gbrowse.conf/plugins/. To install plugins,
    simply copy them into this directory. To uninstall, remove them.

    If you wish to install your own or third party plugins, it is suggested
    that you create a separate directory outside the gbrowse.conf/ hierarchy
    in which to store them and then to indicate the location of these
    plugins using the plugin_path setting:

      plugin_path = /usr/local/gbrowse_plugins

    This setting should be somewhere in the [GENERAL] section of the
    relevant gbrowse configuration file.

  15. THE GENBANK/EMBL PROXY
    Sample configuration number 5 ("05.embl.conf") corresponds to a
    pass-through proxy for Genbank. At least in theory, if you enter a
    landmark that isn't recognized, gbrowse will go to EMBL using the
    bioperl BioFetch facility, parse the record, and enter it into the local
    database. This allows you to browse arbitrary Genbank/EMBL/Refseq
    entries.

    This functionality is not well supported, but here is a recipe for
    giving it a try:

    Create a local database named "embl" and initialize it this way:

    Set up permissions for this database so that "nobody@localhost" has
    SELECT, INSERT, UPDATE and DELETE privileges

    Initialize the database for use with this command:

     % bp_load_gff.pl -c -d embl

    If you need to use a proxy to access remote web sites, uncomment the
    -proxy line in the conf file, and adjust the URL of the proxy as
    appropriate.

    Go to <http://localhost/cgi-bin/gbrowse/embl>. Search for a Genbank or
    embl accession number, such as CEF58D5

  16. REMOVING OUT-OF-DATE IMAGE FILES
    As GBrowse runs, it creates temporary image files in the gbrowse tmp
    directory (typically HTDOCS/gbrowse/tmp). These image files are
    relatively small, but if you run GBrowse for a long time they may begin
    consuming significant amounts of disk space. The following Unix shell
    commands will remove old image files and unused directories:

       cd HTDOCS/gbrowse/tmp
       find . -type f -atime +20 -print -exec rm {} \;
       find . -type d -empty -depth -exec rmdir {} \;

    Be sure to replace HTDOCS with the path to your web server HTML document
    root directory. You might want to run this command under cron, but be
    sure that the user that the cron job runs under has the proper
    permissions. You may need to install it in root's cron script.

  17. THE BALLOON TOOLTIPS
    The balloon tooltip effect requires the balloon javascript files and the
    background balloon images files. You can download them from:

    http://www.wormbase.org/wiki/index.php/Balloon_Tooltips

    Copy balloon.js, yahoo-dom-event.js and prototype.js into the folder:

      $HTDOCS/gbrowse/js

    where $HTDOCS is the path to your apache HTML files. For example, if
    your apache installation path is D:/apache, copy those js files into:

    D:/apache/htdocs/gbrowse/js

    And then copy all balloon image files into the folder:

      $HTDOCS/images/balloons

    Please read CONFIGURE BALLOON TOOLTIPS in CONFIGURE_HOWTO.pod for
    information on how to use this feature.

  18. BUG REPORTS AND SUPPORT REQUESTS
    Please report bugs to the GMOD project bug tracking system at
    <http://sourceforge.net/tracker/?group_id=27707&atid=391291>. EMail
    support is available by sending requests for help to
    gmod-gbrowse@lists.sourceforge.net.

    Have fun!

    Lincoln Stein & the GMOD team