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GBrowse 2.0 Install HOWTO

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This article describes how to install GBrowse 2.0 on either Linux or Mac OSX systems. Before you begin, please make sure that your system has all the GBrowse 2.0 Prerequisites installed. The easiest and most straightforward way to get a basic installation up and running is through the CPAN system, where GBrowse is available as a module that can be installed - see Installing via the CPAN Shell below for more details. This will install the newest stable version of GBrowse.

Advanced users can also install the latest, bleeding-edge, unstable version of GBrowse manually. You will have to build it from the source code available at our SVN code repository - see Installing Manually for a full description of how that process works.

Installing via the CPAN Shell

For a smooth experience, please install all GBrowse 2.0 Prerequisites before proceeding.

You can install the latest released version of GBrowse by running the CPAN shell. Run this command:

sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'

This will run all the steps described in the "Installing Manually" section below, including configuring GBrowse's installation directories and installing GBrowse and its demo databases. Among other things, GBrowse will ask you a series of questions about where to install it. See #Selecting Installation Directories for a detailed description of each question. The suggested defaults are almost always correct.

If any perl modules are missing from the prerequisites, the CPAN shell will install them for you.

Ubuntu 11.04 Issue

The binary version of the GD Perl module that is packaged for Ubuntu 11.04 (Natty Narwhal) contains a bug that causes BioPerl to fail several of its tests, blocking GBrowse installation. To fix:

sudo apt-get remove libgd-gd2-perl
sudo apt-get install libgd2-noxpm-dev
sudo perl -MCPAN -e 'install GD'

Then proceed to install Bio::Graphics::Browser2 as described above.

Installing Manually

Alternatively, you can download and install the bleeding edge version via GIT. For a smooth experience, please install all GBrowse 2.0 Prerequisites before proceeding.

The command to issue is:

git clone https://github.com/GMOD/GBrowse

This will create a directory named Generic-Genome-Browser:

Running the Build.PL Script

Next, enter the newly-created directory and run the Build.PL script:

 % cd Generic-Genome-Browser
 % perl Build.PL
 Checking whether your kit is complete...
 Looks good

 Checking prerequisites...
 Looks good

 cc -I/usr/lib/perl/5.8/CORE -fPIC -c -D_REENTRANT -D_GNU_SOURCE \
   -DTHREADS_HAVE_PIDS -DDEBIAN -fno-strict-aliasing -pipe \
   -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 \
    -O2 -o /tmp/compilet.o /tmp/compilet.c
 cc -shared -L/usr/local/lib -o /tmp/compilet.so /tmp/compilet.o

 Creating new 'Build' script for 'GBrowse' version '2.00'
 Now run:
  ./Build test
  ./Build config
  ./Build demo          (optional)
  ./Build install       (as superuser/administrator)
        -or-
  ./Build install_slave (optional, for slave installations)

Among other things, this script will report all the missing Perl libraries that you need to run GBrowse. Please be sure to install all prerequisites before going any further. To install any missing Perl prerequisites automatically, you may run:

./Build installdeps

After running, Build.PL will create a script named Build in the current directory.

Running the Build Script

You will now use Build to test, configure and install GBrowse. First you will confirm that GBrowse's libraries are completely functional by running ./Build test (the "./" is there to ensure that you are running the Build script in the current directory, and not some other Build script somewhere in your path:

 % ./Build test
 t/01yeast...................ok
 t/02.rearchitecture.........ok
 t/03.render.................ok
 ...
 All tests successful.
 Files=8, Tests=323, 12 wallclock secs
 Result: PASS

All tests should pass (you may safely ignore warnings and occasional timeout errors). If not, please file a bug report, and/or send an inquiry to the GBrowse mailing list.

Selecting Installation Directories

After passings its tests, you should configure GBrowse by running ./Build config:

 % ./Build config

 **Beginning interactive configuration**
 Apache loadable module directory (for demo)? [/usr/lib/apache2/modules]
 Apache CGI scripts directory? [/usr/lib/cgi-bin]
 Directory for GBrowse's config and support files? [/etc/GBrowse2]
 Directory for GBrowse's static images & HTML files? [/var/www/gbrowse2]
 Internet port to run demo web site on (for demo)? [8000]
 User account under which Apache daemon runs? [www-data]

 **Interactive configuration done. Run './Build reconfig' to reconfigure**

The configuration process will ask you to confirm six site-specific configuration options, and will do its best to guess for you. In most cases you can just hit return to accept the default. If you specify a directory that does not exist, the system will ask you to confirm that this is what you mean. If you press yes, the directory (and all its needed parents) will be created at install time.

The configuration options are:

apachemodules
The directory in which Apache's loadable modules are located. This is only needed to run a demo GBrowse site before formal installation. If you do not know the location of this directory and you do not want to run the demo, you can safely ignore this option.
cgibin
The directory in which Apache's executable CGI scripts are located, for example /usr/lib/cgi-bin. This directory is set up for you when Apache is installed, and you must have the path correct in order for Build to install GBrowse's CGI scripts in the right place. GBrowse will be installed into the "gb2" subdirectory, so its path will be "/usr/lib/cgi-bin/gb2/gbrowse".
conf
The location of GBrowse's configuration files. The default is to place them in /etc/gbrowse2. This is where you will go to customize GBrowse and add new data sources.
databases
The default location for GBrowse's in memory databases, and the place where the example databases will be stored. The default is to place this into a subdirectory of the same directory in which GBrowse places its static files, such as /var/www/gbrowse2/databases.
htdocs
The directory in which to install GBrowse's Javascript libraries, static HTML pages and stylesheets. You can choose any location for this directory and it will be added to Apache's document tree. The default is to place the directory under the default document tree, such as /var/www/gbrowse2.
portdemo
The internet port on which the demo will run. The demo launches a new instance of Apache running under your user privileges. Because port 80 will usually already be taken by the system Apache, Build will choose an unused port like 8000 or 8080. You may manually select the port if you wish.
tmp
The directory in which GBrowse will store its working data, including users' session information (such as preferred tracks), uploaded data files, and temporary image files. The default is to place these files into /var/tmp/gbrowse2.
wwwuser
The account under which the system Apache runs, often "nobody", "www-data" or "httpd." If you do not know, you can find out by running ps aux | grep -i apache on a system that has Apache already running. The first column of the output contains the name of the user account.

Once you have configured GBrowse, the values you chose will stick until you run ./Build reconfig. You can also bypass interactive configuration by directly passing Build.PL one or more of the configuration options on the command line:

perl Build.PL --apachemodules=/usr/local/share/apache/libexec \
              --cgibin=/var/lib/cgi \
              --conf=/etc/gbrowse \
              --htdocs=/usr/local/docs/gbrowse \
              --databases=/usr/local/gbrowse/databases \
              --tmp=/tmp/gbrowse \
              --portdemo=9000 \
              --wwwuser=fred

The options passed on the command line will become the defaults for ./Build config will be used during installation, and will also become the defaults if you later run ./Build config or ./Build reconfig.


Here is an example of a 'non-standard' install, that allows you to install and run GB as a non-root user (assuming you have Perl's local-lib working properly):

perl Build.PL \
  --cgibin=$HOME/httpd/cgi-bin/gbrowse2 \
  --conf=$HOME/httpd/conf/gbrowse2 \
  --htdocs=$HOME/httpd/htdocs/potato/gbrowse2 \
  --tmp=$HOME/httpd/tmp \
  --url_base=/potato/gbrowse2

./Build test
./Build install


Note that we still need to tweak $HOME/httpd/conf/gbrowse2/GBrowse.conf to set the 'url_base' from '/gbrowse2' to '/potato/gbrowse2' in this case.

Configure in Mac OS X 10.6.6

If you install apache2 using Mac Ports (http://www.macports.org/).

sh-3.2# ./Build config

**Beginning interactive configuration**
Directory for GBrowse's config and support files? [/etc/gbrowse2] /opt/local/apache2/conf/gbrowse2
Directory for GBrowse's static images & HTML files? [/Library/Webserver/Documents/gbrowse2] /opt/local/apache2/htdocs/gbrowse2
Directory for GBrowse's temporary data [/var/tmp/gbrowse2]
Directory for GBrowse's example databases [/Library/Webserver/Documents/gbrowse2/databases] /opt/local/apache2/htdocs/gbrowse2/databases
Directory for GBrowse's CGI script executables? [/Library/Webserver/CGI-Executables/gb2] /opt/local/apache2/cgi-bin/gb2
Internet port to run demo web site on (for demo)? [80]
Apache loadable module directory (for demo)? [/usr/lib/apache/modules] /opt/local/apache2/modules
User account under which Apache daemon runs? [www]

And after install

sh-3.2# chmod -R 777 /var/tmp/gbrowse2

Copy configure information to the end of '/opt/local/apache2/conf/httpd.conf'

<Directory "/opt/local/apache2/htdocs/gbrowse2">
  AllowOverride Options
  Options -Indexes -MultiViews +FollowSymLinks
  Order allow,deny
  Allow from all
</Directory>

<Directory "/var/tmp/gbrowse2/images/">
  Order allow,deny
  Allow from all
</Directory>

<Directory "/opt/local/apache2/cgi-bin/gb2">

  SetEnv GBROWSE_CONF   "/opt/local/apache2/conf/gbrowse2"
</Directory>

<IfModule mod_fcgid.c>
  Alias /fgb2 "/opt/local/apache2/cgi-bin/gb2"
  <Location /fgb2>
    SetHandler   fcgid-script
    Options      ExecCGI
  </Location>
  DefaultInitEnv GBROWSE_CONF /opt/local/apache2/conf/gbrowse2
  # these directives prevent idle/busy timeouts and may need to be
  # adjusted up or down
  FcgidMinProcessesPerClass 6
  FcgidIOTimeout   600
  FcgidBusyTimeout 600

</IfModule>

<IfModule mod_fastcgi.c>
  Alias /fgb2 "/opt/local/apache2/cgi-bin/gb2"
  <Location /fgb2>
    SetHandler   fastcgi-script
    Options      ExecCGI
  </Location>
  # Note: you may need to increase -idle-timeout if file uploads are timing out and returning server
  # errors.
  FastCgiConfig -idle-timeout 600 -maxClassProcesses 20  -initial-env GBROWSE_CONF=/opt/local/apache2/conf/gbrowse2
</IfModule>

<IfModule mod_perl.c>
   Alias /mgb2 "/opt/local/apache2/cgi-bin/gb2"

   <Location /mgb2>
     SetHandler perl-script
     PerlResponseHandler ModPerl::Registry
     PerlOptions +ParseHeaders
   </Location>
</IfModule>


Running the GBrowse Demo (optional)

Before you install GBrowse, you may wish to run its demo. This will attempt to launch a correctly configured instance of Apache running under your own account. To launch the demo, run ./Build demo:

% ./Build demo
Demo is now running on http://localhost:8000
Run "./Build demostop" to stop it.

You can now point your web browser at http://localhost:8000 (or whatever the build message specifies), and interact with the GBrowse web site, browse sample genomes and otherwise test the waters. When you are done, run ./Build demostop to stop Apache and clean up.

Registering GBrowse (optional)

You may register GBrowse by running ./Build register. This is an optional step, but allows the GBrowse development group to track who is using GBrowse. This information is useful when writing grant renewals :-). The information is only used internally by the GMOD project and is not shared with any other parties.

Final Installation

To install GBrowse and its support files permanently, run ./Build install as the superuser. This will copy GBrowse's library and support files into the locations chosen during configuration. It will then configure Apache to run GBrowse by writing the appropriate configuration directives into Apache's configuration file. Finally, it will attempt to restart Apache. If all goes well, you will see a note telling you to load http://localhost/gbrowse2. This will take you to an autogenerated page that describes the install configurations you chose, points to an example database to run, and gives pointers to documentation, tutorials and other useful information.

Debugging and Customizing the Installation

If you are having trouble with the installation, see Common Problems with GBrowse2 Installation. If you wish install GBrowse in your home directory because you do not have superuser privileges or for any other reasons, see Installing GBrowse2 in your Home Directory. (These pages aren't written yet)!

Advanced Installation Topics

For advanced topics, such as accelerating GBrowse performance by running it under a persistent environment, configuring the user login and custom track upload system, and restricting access to certain databases and tracks via user authentication, see: