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CuffBase

A Django project that takes the output of the tophat/cufflinks pipeline, builds an SQL database (by default MySQL) in much the same way cummeRbund does and makes it available through the Web interface. Unlike cummeRbund, multiple pipeline runs can be stored in the same database.

The primary goal of CuffBase is to make the results of cuffdiff pipeline accessible to a bench scientist.

Provides very limited plotting facilities via matplotlib.

Dependencies

Deployment

The recommended way to deploy CuffBase is to setup mod_wsgi in Apache2 or Gunicorn behind Nginx server. See ngs/settings.py file for the settings that need to be configured.

Quick start

You need to set up your database and specify relevant information (backend, username, and password) in the ngs/settings.py file before trying to import cuffdiff output results. For example, if using MySQL:

mysql> create database <database-name> default charset utf8 collate utf8_general_ci;
mysql> grant all on <database-name>.* to <user>@localhost identified by <password>;

and then the databases section of your ngs/settings.py file should read:

DATABASES = {
    'default': {
        'ENGINE': 'django.db.backends.mysql',
        'NAME': '<database-name>',
        'USER': '<user>',
        'PASSWORD': '<password>',
        'HOST': '',                      # Empty for localhost through domain sockets or '127.0.0.1' for localhost through TCP.
        'PORT': '',                      # Set to empty string for default.
    }
}

to load the example database from the provided sql dump:

$ gunzip -c ngs-dump-1.gz | mysql -u<user> -p<password> <database-name>

to import the cuffdiff output run this from the cuffbase directory:

$ ./manage.py import_exp <path-to-cuffdiff-output>

to see available options for the import_exp command:

$ ./manage.py import_exp --help

to start development server locally run this from the cuffbase directory:

$ ./manage.py runserver --insecure

and cuffbase should be accessible in your browser at http://localhost:8080/cuff

Caveats and limitations

I did my best trying to stick as close to the original cummeRbund database schema as possible. I had, however, to use integer pks instead of string pks in cummeRbund to make it play nicely with Django ORM. In addition, PhenoData, Feature, and Attribute tables are basically placeholders. Not sure what to make of them.

  • no tests -- the project was concieved as an ad-hoc solution with little consideration for future maintenance (I wasn't sure it'd work at all!)
  • tests are sorely needed -- will be the first priority in moving forward
  • no docs -- same as the tests
  • not tested with anything but MySQL 5.5
  • it was only tested on full cuffdiff output

Future plans

  • interactive plotting with Bokeh
  • tests
  • docs (mostly on deployment)
  • port to Python 3 (should be easy?)
  • IPython notebook integration?