-
Notifications
You must be signed in to change notification settings - Fork 8
Download & Installation
Complete source code for Trait-o-matic is now available in the repository but lacks thorough commenting. The following are instructions detailing how code from the repository can be used to install a fully working mirror.
From a fresh install of Ubuntu (Hardy Heron) on a virtual node with AMD64 processors, the following commands were issued:
Configuration of Apache and Sendmail settings then took place. In particular:
- In
/etc/hostname
, the existing hostname was deleted and replaced by the fully qualified hostname - In
/etc/hosts
, the fully qualified hostname was inserted before the existing hostname - In
/etc/mail/sendmail.mc
, the existing hostname was deleted and replaced by the fully qualified hostname in theMASQUERADE_AS
option, and all features were moved beforeMAILER_DEFINITIONS
- In
/etc/apache2/sites-available/default
,ServerSignature On
was replaced byServerSignature Off
- In
/etc/apache2/sites-available/default
, the following was added and/or modified:
- In
/etc/php5/apache2/php.ini
, the following settings were modified to those values indicated below:
The following commands were then issued:
sudo chown www-data:www-data /var/www sudo chmod 777 /var/www sudo apache2ctl graceful sudo sendmailconfig
Trait-o-matic source can be retrieved by downloading from GitHub; core components were extracted and copied to /usr/share/trait
, the necessary Pyrex extensions were compiled in-place, and then the XMLRPC init script (by which Trait-o-matic responds to requests) was copied to the correct directory and installed:
Databases, database users, and database tables were created for access to MySQL (note that it is advised to change the password from the default shakespeare
, and that the file /usr/share/trait/config.py
must be updated accordingly). The SQL commands issued were as follows:
Reference genome data were retrieved in 2bit format from UCSC and saved to the path indicated in /usr/share/trait/config.py
(by default, /var/trait/hg18.2bit
) and other data to be stored in database tables were retrieved from their respective sources:
Data tables were loaded with the following MySQL commands:
It is a peculiarity of the current storage system that permanent files are by default stored in /tmp
; with a second volume mounted at /scratch
with more ample storage space, /tmp
was then moved to /scratch/tmp
and configured not to be wiped on reboot:
sudo mv /tmp /scratch/tmp sudo ln -s /scratch/tmp /tmp sudo sed -i'.bak' 's/TMPTIME=0/TMPTIME=-1/' /etc/default/rcS
Then, the Trait-o-matic core XMLRPC server was started:
sudo /etc/init.d/trait.sh start
CodeIgniter (1.7.1) was downloaded and installed. (Note: web components are compatible with CodeIgniter versions 1.7.0 and 1.7.1; other versions have not been tested.)
cd wget http://codeigniter.com/download.php unzip CodeIgniter_1.7.1.zip cd CodeIgniter_1.7.1 sudo cp index.php /var/www sudo cp -R system /var/www/system sudo mv -i /var/www/index.html /var/www/index.html.default
Then, Trait-o-matic web components were copied into the correct directories:
cd sudo cp -R xwu-trait-o-matic-*/web/errors /var/www sudo cp -R xwu-trait-o-matic-*/web/media /var/www sudo cp -R xwu-trait-o-matic-*/web/scripts /var/www sudo cp -R xwu-trait-o-matic-*/web/statistics /var/www sudo rm -Rf /var/www/system/application sudo cp -R xwu-trait-o-matic-*/web/system/application /var/www/system/application sudo cp xwu-trait-o-matic-*/web/htaccess /var/www/.htaccess
Finally, /var/www/system/application/config/config.php
was configured with the correct domain name. Additionally, database.php
and upload.php
were checked and updated with any necessary changes in setting.