INSTALL

This instructions relate to the installation of the eFORGE webserver.

This is based on a VM running Scientific Linux with Perl 5.10.1. You may need to adapt these
commands if you wish to install the webserver on a different system.

Step-by-step guide
==================

1. Log into the VM
------------------

    ssh USER@eforge.cs.ucl.ac.uk

2. Download the eForge package and install the dependencies
-----------------------------------------------------------

2.a. The code lives in GitHub and the databases and mvp_*_bins files are available through the
webserver.

    cd
    
    git clone https://github.com/charlesbreeze/eFORGE.git
    
    cd eFORGE

    wget http://eforge.cs.ucl.ac.uk/files/eforge.db
    wget http://eforge.cs.ucl.ac.uk/files/eforge_1.1.db
    wget http://eforge.cs.ucl.ac.uk/files/eforge_1.2.db
    wget http://eforge.cs.ucl.ac.uk/files/mvp_450k_bins
    wget http://eforge.cs.ucl.ac.uk/files/mvp_27k_bins

2.b. Install Perl dependencies

Just test the code

    perl eforge.pl

and install the missing packages using cpan.

    sudo cpan -i Sort::Naturally
    sudo cpan -i Config::IniFiles
    sudo cpan -i Data::UUID
    sudo cpan -i Statistics::Multtest

2.c. Install R and R packages rjson, rCharts and RSQLite (for the log):

    sudo yum install R

    sudo R
 
    install.packages("rjson");
    install.packages("devtools"); # In case you don't have this in your system
 
    require(devtools);
    install_github('ramnathv/rCharts');
 
    install.packages("RSQLite")


2.d. Run the software and test that you get the PDF and the dimple chart:

    perl eforge.pl

You must find a new directory called "0x*" with several files, including a .pdf and a  .dchart.html.
Check that these work. If the .dchart.html cannot be open. By default, the HTML links to the
location of the js code on the local machine. For the server, this should point at a public URL
server by the server itself.

3. Install the web server
-------------------------

3.a. Install the Apache package if required:

    sudo yum install httpd.x86_64

3.b. Create some directories for hosting the code, log and result files:

    sudo mkdir /var/www/eFORGE.v1.2/
    cd /var/www/eFORGE.v1.2/
    sudo mkdir -p bin log cgi-bin html html/files
    sudo chown apache log html/files # the user under which you run apache (see the line "User" in
                                     # /etc/httpd/conf/httpd.conf)

3.c. Copy the webserver files to the right directories 

    sudo rsync -avPL ~/eFORGE/webserver/cgi-bin/ /var/www/eFORGE.v1.2/cgi-bin/
    sudo rsync -avPL ~/eFORGE/webserver/bin/ /var/www/eFORGE.v1.2/bin/
    sudo rsync -avPL ~/eFORGE/webserver/html/ /var/www/eFORGE.v1.2/html/
    sudo rsync -avPL ~/eFORGE/eforge.db /var/www/eFORGE.v1.2/bin/
    sudo rsync -avPL ~/eFORGE/eforge_1.1.db /var/www/eFORGE.v1.2/bin/
    sudo rsync -avPL ~/eFORGE/eforge_1.2.db /var/www/eFORGE.v1.2/bin/
    sudo rsync -avPL ~/eFORGE/mvp_450k_bins /var/www/eFORGE.v1.2/bin/
    sudo rsync -avPL ~/eFORGE/mvp_27k_bins /var/www/eFORGE.v1.2/bin/

3.e. Add links to the database files for the Downloads page:

    cd /var/www/eFORGE.v1.2/html/files
    sudo ln -s ../../bin/eforge.db .
    sudo ln -s ../../bin/eforge_1.1.db .
    sudo ln -s ../../bin/eforge_1.2.db .
    sudo ln -s ../../bin/mvp_450k_bins .
    sudo ln -s ../../bin/mvp_27k_bins .

3.f. Create the configuration files

These files contain a list of arrays and dataset included in the database. They are used by the
web server to know what it can offer without having to query the DB every time.

    cd /var/www/eFORGE.v1.2/bin
    perl eforge.pl -data ? > data.conf
    perl eforge.pl -bkgd ? > bkgd.conf

3.g. Configure the Apache server

You can choose to either run eFORGE on a VirtualHost (like http://eforge.cs.ucl.ac.uk/) or on a
folder (like http://blic.cs.ucl.ac.uk/eFORGE).

OPTION 1 -- Configure an Apache VirtualHost for eFORGE:

    cat > /etc/httpd/conf.d/eforge.v1.2.conf
<VirtualHost *:80>
    ServerName eforge.cs.ucl.ac.uk
    DocumentRoot /var/www/eFORGE.v1.2./html
    ScriptAlias /cgi-bin/  /var/www/eFORGE.v1.2/cgi-bin/

    <IfModule dir_module>
        DirectoryIndex index.html /cgi-bin/index.pl
    </IfModule>

    <Directory "/var/www/eFORGE.v1.2/html">
        Order allow,deny
        Allow from all
    </Directory>

    <Directory "/var/www/eFORGE.v1.2/cgi-bin">
        AllowOverride None
        Options None
        Order allow,deny
        Allow from all
    </Directory>
</VirtualHost>


OPTION 2 -- Configure an Apache VirtualHost for eFORGE:

    cat > /etc/httpd/conf.d/eforge.v1.2.conf
ScriptAlias /eFORGE.v1.2/cgi-bin/  /var/www/eFORGE.v1.2/cgi-bin/
Alias "/eFORGE.v1.2" "/var/www/eFORGE.v1.2/html"

<Directory "/var/www/eFORGE.v1.2/html/">
    Order allow,deny
    Allow from all

    DirectoryIndex index.html cgi-bin/index.pl
</Directory>

<Directory "/var/www/eFORGE.v1.2/cgi-bin/">
    AllowOverride None
    Options None
    Order allow,deny
    Allow from all
</Directory>


3.h. Copy the rCharts libraries to the html path:

    sudo rsync -avP /usr/lib64/R/library/rCharts/libraries /var/www/eFORGE.v1.2/html/

3.i Re-start Apache

    sudo /etc/init.d/httpd restart