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Generic Genome Browser Installation


    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 --
        The MySQL database is a fast open source relational database that is
        widely used for web applications. It is required for most real-live
        genome annotation projects. 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 --
        The Apache web server is the industry standard open source web
        server for Unix and Windows systems.

    C) Perl 5.005 --
        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 --
        The following Perl modules must be installed for GBrowse to work.
        They can be found on the Comprehensive Perl Archive Network (CPAN):


    E) Bioperl version 1.2.2 or higher --
    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

    G) LWP
        To load remote 3d party annotations.


    Make sure that Apache and a database (MySQL, Oracle or PostgreSQL) are
    installed before you start.

    Brief synopsis:

    For PPM3:

            ppm> rep add gmod
            ppm> rep up gmod
            ppm> rep up gmod
            ppm> install DBD::mysql (or DBD::Pg or DBD::Oracle)
            ppm> install Generic-Genome-Browser

    for PPM2:

            add ppm synopsis here

    Binary distributions of GBrowse and the 1.2.2 version of Bioperl live at Add this repository to the list of active
    repositories, and then move the repository to the top to ensure that you
    get the most up to date versions of the modules.

    If you wish to use a MySQL database, install DBD::mysql if you have not
    already done so. Then install Generic-Genome-Browser.

    At the end of the install, the automatic installation script will ask
    you to confirm the locations of your Apache conf (configuration), htdocs
    (document root) and cgi-bin (CGI executable) directories. Usually it
    will guess right, but if it doesn't, just type in the correct path.

    When this is done, go to step (4) below.


    Skip this step if you have installed with ActiveState's PPM.

    Brief synopsis:

            perl Makefile.PL
            make install

    The last step may need to be done as root. There is a test defined for
    this package, but you must initialize and load a database before you can
    run it.

    This will install the software in the default location under
    /usr/local/apache. See "Details" to change this.

    To further configure GBrowse, see the CONFIGURE_HOWTO manpage. To run
    GBrowse on top of Oracle, PostgreSQL and BioSQL databases see the
    ORACLE_AND_BIOSQL manpage. To run GBrowse on top of Gadfly, see the
    README-berkeley-gadfly manpage.


    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. By default, these will be installed in the following

       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

    The following arguments are recognized:

      CONF Configuration file directory
      HTDOCS Static files directory
      CGIBIN CGI script directory
      INSTALLSITELIB Perl site-specific modules directory
      PREFIX Base directory for conf, htdocs and cgibin

    For example, if you are on a RedHat system, where the default Apache
    installation uses /var/www/html for HTML files, /var/www/cgi-bin for CGI
    scripts, and /etc/httpd/conf for the configuration files, you should
    specify the following configuration:

      perl Makefile.PL HTDOCS=/var/www/html \
                       CONF=/etc/httpd/conf \

    (The backslashes are there to split the command across multiple lines
    only). To make it easier when upgrading to new versions of the software,
    you can put this command into a shell script.

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

      perl Makefile.PL PREFIX=/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

    You can always manually move the files around after install. See the
    CONFIGURE_HOWTO manpage 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 /usr/local/apache/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 use the


    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:


    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

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

    More configuration information and a short tutorial are located at:



    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).


      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' -d yeast sample_data/yeast_data.gff
      make test


    Note for RedHat Linux users: note that if you are using the default
    installed Apache, the user that apache runs as is 'apache' as opposed to
    the otherwise standard 'nobody'. Therefore, everywhere 'nobody' occurs
    in these directions, replace it with 'apache'.

    In Bioperl versions 1.3 or later (not released as of August 2003), this
    script is named

    You will need a MySQL database in order to start using GBrowse. 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

    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:

        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.

        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, but does not work in the
        situation in which the MySQL database is running on a remote host.

        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. Earlier versions of the distribution
    will have these files directly in the scripts/ subdirectory.

    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:

    Load the file with this command: -d yeast -fasta yeast.fasta.gz </dev/null

    (or, if you are on a windows system: -d yeast -fasta yeast.fasta.gz

    and hit ^Z when the script pauses.)

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

    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.


    Genome feature tables for the major model organisms and human can be
    found at in the downloads section, but these files are not
    guaranteed to be up to date.

    Each model organism database has its own flat file format for
    representing the data. For the most up to date information, you should
    download these files and process them into GFF format. Currently, all of
    the model organism databases require some tweaking of the flat files,
    but the bioperl distribution includes several small perl scripts to make
    this easier. These scripts are optionally installed when you install
    Bioperl. You'll find them in the bioperl scripts/Bio-DB-GFF directory if
    you didn't install them directly.

    They are: For FlyBase D. melanogaster flat files For human annotations from NCBI For SGD S. cerevisiae flat files For WormBase C. elegans flat files

    In Bioperl 1.3, these scripts are named, and so

    Run the script with the -h option to get some data-specific help:

      % -h

    The script requires the AcePerl package, which is
    available from CPAN. It is not strictly necessary to run this script
    because the unaltered GFF files distributed from WormBase are compatible
    with GBrowse. supplements the information with the
    physical positions of genetic markers, GenBank accession numbers and
    functional descriptions of gene products.

    For configuration files that will work with each of these databases,
    look in contrib/conf_files (or in
    http://localhost/gbrowse/contrib/conf_files). Simply copy the
    appropriate configuration file into your gbrowse.conf directory, and
    edit the database name as appropriate.

    You might also be interested in the script, which is
    installed when you install GBrowse. You can give this script a list of
    Genbank or EMBL accession numbers and it will automatically download the
    indicated entries and load them into a MySQL database. You can also load
    flat files in Genbank or EMBL format.

    The sample configuration file 08.genbank.conf (located in
    contrib/conf_files) is appropriate for data loaded with


    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 or 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: -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

    Run " -h" to see usage instructions.


    See the file doc/configuration.txt 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.


    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), I recommend that you install the mod_perl module for
    Apache. ( 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 from the gbrowse.conf/plugins

    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. I 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 the CONFIGURE_HOWTO manpage). 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.


    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.


    GBrowse is evolving quickly, and some of its features are dependent on
    new features in Bioperl 1.2.2. If you are having trouble making GBrowse
    run, make sure you are using Bioperl 1.2.2!


    The gbrowse_img CGI script (a new feature as of version 1.41), 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=";name=mec-3">
        <img src=";name=mec-3;width=200">

    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.

    Read docs/gbrowse_img.txt DOES NOT EXIST for the CGI parameters and
    other instructions. A copy of these instructions in HTML form will be
    generated when gbrowse_img is called without any arguments. Type into your favorite web browser.


    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.


    Sample configuration number 5 ("05.embl.conf") corresponds to an
    experimental 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

    You are free to experiment with this, but don't expect it to be entirely
    reliable. To get it to work, you must:

    1 Make sure you are using Bioperl 1.02 (or a patched version of 1.01)

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

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

    4 Initialize the database for use with this command:

          % -c -d embl </dev/null

        (if you are on a windows system, just leave out the </dev/null)

    5 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

    6 Go to http://localhost/cgi-bin/gbrowse?source=embl. Search for a
        Genbank or embl accession number, such as CEF58D5


    When updating GBrowse to a new version of the software, you can
    configure it using your preferred directory settings by making a backup
    copy of the file GGB.def that was generated the first time you installed
    GBrowse and using `cat GGB.def` as the argument to Makefile.PL. Here is
    the recipe:

      cp Generic-Genome-Browser-1.40/GGB.def Generic-Genome-Browser-1.41/GGB.def
      cd Generic-Genome-Browser-1.41/
      perl Makefile.PL `cat GGB.def`
      make install


    Currently there is one known bug. The navigation buttons do not operate
    properly when the client is using Internet Explorer 5.1 on a Macintosh
    and accessing gbrowse running on a MacOS X server running Apache. Other
    combinations of clients and servers work properly.

  17. FEATURE WISH LIST (updated June 6, 2003)

     - Full DAS support.
     - A glyph for representing cytogenetic maps.

    If you are interested in working on any of these features, please
    contact the developers at the address given in the next section.


    Please send requests for help to
    There is also a formal bug tracking and feature request system in place

    Have fun!

    Lincoln Stein & the GMOD team

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