======================== Dependencies ======================== - php 5.0 - mysql 5.1 - php-xml - python >= 2.x - EMBOSS - MySQLdb for python ==================== Install ==================== To install you need to configure the installation in the file install.config. Please remember that we encourage that you create an empty database before installing the application. After editing install.config, just run: $ bash install.sh An follow the steps. Note that you'll probably don't need to install as root, depending on the directories you pass on install.config. ====================== Extra steps ====================== The next few tips are only needed when the main install script failed or was not configured to do so. To manually install the garbage collector cron job: $ crontab -e and append: 0 0 * * * /usr/bin/python $(PWD)/scripts/gc_subsequences.py To manually install the NCBI taxonomy database, you should do: cd scripts && sh ncbi.sh <database password> To use some EMBOSS tools you need to create the PRINTS database: # sudo sh generate_prints.sh To use some EMBOSS tools you need to create the PROSITE database: # sudo sh generate_prosite.sh To install labels that were not installed during installation you run some of the following scripts: # python script.py label_antigenic.py label_letters.py label_sigcleave.py label_chips.py label_epestfind.py label_patmatmotifs.py label_iep.py label_pscan.py label_others.py ========================== PHP/MySQL considerations ========================== In some installations, PHP only allows uploads up to 2MB, if you want to upload bigger sequence files please change upload_max_filesize and post_max_size in php.ini and reset the HTTP server. Note that post_max_size should be greater than upload_max_filesize. In the [PHP] section of /etc/php.ini you can use for example: post_max_size = 32MB upload_max_size = 16MB For MySQL we recommend activating the query cacher, by setting in /etc/my.cnf the following variables in the section [mysqld]: query_cache_type=1 query_cache_size=67108864 # 64MB