Web application to load, annotate, parse, search, and display annotated Variant and Mutation data
###Debian/Ubuntu:
- xvfb - required for driving headless instance of Firefox for web-scraping
- Firefox
###Python:
- Django==1.7.4
- EasyProcess==0.1.9
- PyVirtualDisplay==0.1.5
- argparse==1.2.1
- beautifulsoup4==4.3.2
- django-admin-bootstrapped==2.3.2
- django-crontab==0.6.0
- django-extensions==1.5.2
- django-password-reset==0.7
- ipython==3.1.0
- mysqlclient==1.3.5
- pydot==1.0.2
- pygraphviz==1.2
- pyparsing==1.5.7
- pytz==2014.10
- requests==2.6.0
- selenium==2.47.0
- simplejson==3.6.5
- six==1.9.0
- tablib==0.10.0
- uWSGI==2.0.10
- wsgiref==0.1.2
Place the viewer directory into your new or pre-existing site directory, then make the following updates and additions.
# Application definition
INSTALLED_APPS = (
'django_admin_bootstrapped',
'django.contrib.admin',
'django.contrib.auth',
'django.contrib.contenttypes',
'django.contrib.sessions',
'django.contrib.messages',
'django.contrib.staticfiles',
'viewer',
'django_extensions',
'django_crontab',
'password_reset',
)
# EMAIL and SMTP settings
EMAIL_USE_TLS = True
EMAIL_HOST = 'smtp.someservice.com'
EMAIL_PORT = 587
EMAIL_HOST_USER = 'joe@email.add'
EMAIL_HOST_PASSWORD = email_host_password
DEFAULT_FROM_EMAIL = EMAIL_HOST_USER
# Database
# https://docs.djangoproject.com/en/1.7/ref/settings/#databases
DATABASES = {
'default': {
'ENGINE': 'django.db.backends.mysql',
'OPTIONS': {
'read_default_file': BASE_DIR + '/igsb_report_viewer/my.cnf',
},
}
}
# Cronjobs
CRONJOBS = [
('10 2 * * *',
'viewer.links_out.cron.gather_md_anderson')
]
# Static file and media links
STATIC_URL = '/static/'
MEDIA_ROOT = BASE_DIR + '/viewer/files/'
MEDIA_URL = '/viewer/files/'
LINKS_OUT = BASE_DIR + '/viewer/links_out/'
LOGIN_URL = '/viewer/login/'[client]
database = report_viewer
user = dbusername
password = dbpassword
host = dbhost
default-character-set = utf8urlpatterns = patterns('',
url(r'^admin/', include(admin.site.urls)),
url(r'^viewer/', include('viewer.urls')),
url(r'^password_reset/', include('password_reset.urls')),
)Under the groups section, select "Add Group", then apply these permissions:
- Caller, Genome
- Add
- Project
- Add
- Change
- Study, Sample, Bnid, Report, Variant
- Add
- Change
- Delete
Every user that registers must be added to the project_user group to be able to use the application.
NOTE: Don't forget to create your django superuser account first.