/dmd-interpreter

DMD Open-access Variant Explorer (DOVE): A tool to aggregate clinically relevant information related to variants in the DMD gene.

Primary LanguagePython

DMD Open-access Variant Explorer

Contributors: Mitch Bailey, Nicole Miller, Ivo Fokkema

Purpose

The purpose of the DMD Open-Access Variant Explorer (DOVE) is to streamline analysis of genetic variants effecting the Dp427m (NM_004006.2) transcript of the DMD gene.

DOVE uses Python and the Django web framework to integrate existing open-access tools to reduce the number od distinct searches needed to analyse a variant, and to expand analysis beyond variants already well described (i.e. novel variants). In addition to predicted consequences of genetic variants, the tool integrates theoretical eligibility for exon skipping or read-through therapies.

Set up

  • Requires Python2.7, corresponding pip, virtualenv, Perl.

  • Clone/download dmd-interpreter then cd to the dmd-interpreter directory.

  • Create and activate the virtual environment:

    virtualenv DOVE_env --python=python2.7
. DOVE_env/bin/activate

  • Download all dependencies:

    pip install -r requirements.txt

  • To run locally (suggestions/contributions are welcomed!):

    ./manage.py runserver 0.0.0.0:8000

    Note: For static files to be served locally, DEBUG will need to be TRUE in settings.py.

  • DOVE can now be tested through your browser. To deactivate:

    deactivate
exit

Installing DOVE on an Apache2 environment

  • Requires libapache2-mod-wsgi.

  • Edit Apache's .conf file for the site you wish to add DOVE to.

  • Add the following lines to your Apache config (don't forget to change the paths):

    Alias /static /var/www/dmd-interpreter/interpreter/static
<Directory /var/www/dmd-interpreter/interpreter/static>
    Require all granted
</Directory>

<Directory /var/www/dmd-interpreter/interpreter_site>
    <Files wsgi.py>
        Require all granted
    </Files>
</Directory>

WSGIDaemonProcess DOVE python-home=/var/www/dmd-interpreter/DOVE_env home=/var/www/dmd-interpreter
WSGIProcessGroup DOVE
WSGIScriptAlias /DOVE /var/www/dmd-interpreter/interpreter_site/wsgi.py

  • Make sure Apache has rights to write to the temp file (interpreter/temp.txt) and the triage html file (interpreter/templates/triage.html).

  • Restart Apache to complete the process.

View at LUMC: http://www.dmd.nl/DOVE