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Django web interface for Quast assembly assessment tool: https://github.com/ablab/quast
ablab/quast-website
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*************************************************** FIRST INSTALLATION *************************************************** Pre-intallations Ubuntu: $ sudo apt-get install sqlite3 $ sudo apt-get install python-dev $ sudo apt-get install libevent-dev # sudo apt-get install MySQL-python Mac OS: $ brew install sqlite3 $ brew install libevent $ export CFLAGS=-I/brew/include $ mkdir quast $ cd quast Clone command line quast application: $ git clone --recursive https://github.com/ablab/quast-website.git source $ cd source $ git submodule init $ git submodule update Install python virtual environment: $ easy_install pip $ pip install virtualenv $ virtualenv virtualenv $ source virtualenv/bin/activate $ pip install -r source/pip_requirements.txt # Installs dependencies listed in the file. In my case, for sqlalchemy sudo was reqiured, so if something is not working, try 'sudo pip install sqlalchemy' Initialize database: $ source/manage.py migrate Start celery that will process tasks $ source/manage.py celeryd (if running locally) start Django test webserver: export DEVELOPMENT=1 $ source/manage.py runserver localhost:8000 (if on a web server) configure Apache: Create an Apache configuration file in /etc/apache2/sites-available/quast containg the folling. Please replace ServerName and paths starting with '/var/www/quast' according to your environment) <VirtualHost *:80> ServerAdmin webmaster@localhost ServerName quast.bioinf.spbau.ru DocumentRoot /var/www/quast/source <Directory /var/www/quast/source> Options FollowSymLinks MultiViews AllowOverride None Order allow,deny allow from all </Directory> ErrorLog ${APACHE_LOG_DIR}/quast-error.log # Possible values include: debug, info, notice, warn, error, crit, # alert, emerg. LogLevel warn CustomLog ${APACHE_LOG_DIR}/quast-access.log combined Alias /static/ /var/www/quast/source/static/ <Directory /var/www/quast/source/static> Order deny,allow Allow from all </Directory> WSGIDaemonProcess quast user=saveliev group=www-data python-path=/var/www/quast/virtualenv/lib/python2.7/site-packages WSGIProcessGroup quast WSGIScriptAlias / /var/www/quast/source/wsgi.py <Directory /var/www/quast/source> <Files wsgi.py> Order deny,allow Allow from all </Files> </Directory> </VirtualHost> Start apache $ sudo apachectl start *************************************************** DEPLOYING CHANGES *************************************************** $ cd source Locally push everything to Github: $ git all $ git commit -m '[comment]' $ git up $ git push On the server, pull changes: $ git pull Collect static files: # source/manage.py collectstatic Gracefully restart Apache: $ sudo apachectl graceful If you want to pull latest changes for the command-line Quast, $ cd quast $ git pull $ cd .. $ cd git all $ cd commit -m 'Updated command-line Quast' $ cd push On the server: $ git pull $ source/manage.py collectstatic Interrupt celery and start again: $ source/manage.py celeryd $ sudo apachectl graceful Note that data and virtualenv directories are kept different for development and deployment.
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