= Telomere Length Recording Application HowTo Install

Tags: [[Telomere Length Recording Application]] [[HowTo]] [[Install]] [[Pain in the proverbial]] [[UoL LAMP Server]]

== Requirements

Before installation can start, the following packages will have to be installed by IT services:

- libmysqlclient-dev
- python-dev
- libldap2-dev
- libsasl2-dev

== Difficulties

This installations is made more difficult by 3 things:

1. Suse Linux does not have mod_wsgi in its repositories, so you're going to have to compile it.
2. mod_wsgi seems picky about where it picks python apps and libraries from
3. The LAMP servers don't put things where you'd expect them to be.
4. Some other stuff that I don't quite understand

== Start Services

Start the Apache and MySQL and make sure that they are restarted when the server is rebooted.

{{{
sudo /sbin/chkconfig uol.apache2 on
sudo /etc/init.d/uol.apache2 start
sudo /sbin/chkconfig uol.mysql on
sudo /etc/init.d/uol.mysql start
}}}

== Proceduce

1. [[HowTo Compile mod_wsgi for LAMP servers]]
2. Copy the Telomere application from the `git` repository into `/local/` directory.
3. Install virtualenv:

{{{
easy_install --install-dir=/local/python virtualenv
}}}

    ''For some reason that I can't work out (point 4. above), it would only pick up some of the python libraries from a virtual env and not when they were installed in `/local/python/`.  Maybe this was because of the order that I installed things, but I couldn't get it to work without the virtual environment.''
4. Create a virtual environment in the telomere application directory.

{{{
cd /local/telomere
/local/python/virtualenv --no-site-packages BASELINE
}}}

    ''`BASELINE` is the name of the virtual environment.  It could be called anything, but it's called that!  Also note that you need to use the full path to the `virtualenv` utility, since `/local/python` isn't in `$PATH`.''

5. Activate the environment, install the required packages, then deactivate:

{{{
source BASELINE/bin/activate
easy_install flask
easy_install flask-sqlalchemy
easy_install mysql-python
easy_install flask-login
easy_install python-ldap
easy_install flask-wtf
easy_install WTForms-Components
easy_install openpyxl
deactivate
}}}

6. Load the WSGI module into Apache, by editing the file `/local/apache2/etc/loadmodule.conf` by adding this line at the end.

{{{
LoadModule wsgi_module /local/apache2/etc/mod_wsgi.so
}}}

    ''This presumes that you've copied the compiled `mod_wsgi.so` file into the `/local/apache2/etc/` directory.''

7. Add the WSGI config to the Apache config file `/local/apache2/etc/httpd.conf`:

{{{
<Directory /local/telomere>
    WSGIProcessGroup telomere
    WSGIApplicationGroup %{GLOBAL}
    Order deny,allow
    Allow from all
</Directory>

WSGIDaemonProcess telomere user=wwwrun threads=5 python-path=/local/telomere/BASELINE/lib/python2.6/site-packages:/local/python:/usr/lib64/python2.6/site-packages:/usr/share/doc/packages/ home=/local/telomere/
WSGIScriptAlias / /local/telomere/app/telomere.wsgi
}}}

    ''The two hard won things here are the values for the `python-path` and `home` arguments.  The `python-path` must contain every directory where python libraries are installed, including a sub-directory of the virtualenv directory you created earlier.  The `home` must point to your application directory, or you won't be able to pick up your own modules.''

8. Restart apache:

{{{
sudo /etc/init.d/uol.apache2 restart
}}}

9. Pray.

== Other Possible Stuff

1. You may need to give `wwwrun` extra permissions to the `/local/telomere` directory.
2. You might need to pray a bit more.

== Permission to Upload Directory

1. In order to upload spreadsheets, you need to create an upload directory, for example `/local/telomere/uploads`.
2. You then need to point to this in the settings.py file `SPREADSHEET_UPLOAD_DIRECTORY = '/local/telomere/uploads'`
3. Finally, you need to give `wwwrun` permission to read and write to the directory.

{{{
setfacl -m u:wwwrun:rwx /local/telomere/uploads/
setfacl -m d:u:wwwrun:rwx /local/telomere/uploads/
}}}

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