Installation of abstrackr on a shared host (Site5)

Shared hosting is cheap but you don't have root access to mysql or the ability to add server-wide python modules. Luckily you can still run abstrackr on a shared host by using a virtual environment. These are the steps I took to install abstrackr on a Site5 shared hosting package - they could work for other shared hosting providers.

1. Login to the Site5 control panel and create a new database and user in the SiteAdmin control panel - make a note of the name of the database, the user and the password.

2. Now login to your site5 server using ssh (make sure you enable ssh access first in the control panel) and cd to your home directory

cd ~

3. Download virtualenv from https://pypi.python.org/pypi/virtualenv and extract it

wget https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.10.1.tar.gz --no-check-certificate
tar -zxvf virtualenv-1.10.1.tar.gz
cd virtualenv-1.10.1

4. create a virtual environment called (for example) myVE in the home directory and then activate it

python2.6 virtualenv.py ~/myVE
cd ~/myVE/bin
source activate

5. Create the project root folder in your home directory (I called mine "abstrackr").

cd ~
mkdir abstrackr
cd abstrackr

6. Install eutils

git clone https://github.com/hpiwowar/eutils
cd eutils
python setup.py build
python setup.py install
cd ..

7. Install PyGoogleChart, Numpy, Biopython and Abstrackr

pip install pygooglechart
pip install numpy
pip install "biopython==1.57"
easy_install abstrackr

8. Install Flup

easy_install flup

9. Copy the sample ini file to the project root folder. I called my ini file "live.ini" - (you will need to refer to this ini file in your Fast CGI server file in a couple of steps time).

10. Edit the ini file - changing the database name and password to the one you created. Change smtp_host and smtp_port to your own settings (check the Site5 SiteAdmin client e-mail information). I had to use port 2525 on Site5. Make sure debug is set to FALSE.

11. I also added the following lines to my ini file - I'm not sure if it is strictly necessary

[server:main]
use = egg:Flup#fcgi_thread
host = 0.0.0.0
port = 6500

12. Now you need to build your database tables. Run the following command on your ini file from the 'project root' directory. My ini file is called "live.ini".

paster setup-app live.ini

13. create a Fast CGI server file in the ~/public html directory to deploy abstrackr (I called mine "index.fcgi"). Substitute YOURUSERNAME for your own username! Change the permissions on this server file to 755.

#!/home/YOURUSERNAME/myVE/bin/python2.6
import sys

from paste.deploy import loadapp
from flup.server.fcgi_fork import WSGIServer

app = loadapp('config:/home/YOURUSERNAME/abstrackr/live.ini')
server = WSGIServer(app)
server.run()

14. Add following lines to the .htaccess file in your ~/public_html directory

Options +ExecCGI
AddHandler fcgid-script .fcgi
Options +FollowSymLinks

RewriteEngine On
RewriteBase /
RewriteRule ^index\.fcgi/index\.fcgi(.*)$ index.fcgi/$1 [L]
RewriteRule ^index\.fcgi/ - [L]
RewriteRule ^(.*)$ index.fcgi/$1 [L]

15. If you want to upgrade to the development version of abstrackr, then activate your virtual environment (as in step 4) then type the following command:

easy_install --upgrade abstrackr