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CaPSID Pipeline

CaPSID's pipline is available as a package in the Python Package Index.

Dependencies

In order to run CaPSID's pipeline, you will need to install the following dependencies:

  • Python - Python 2.6+ supported. No support for Python 3 at the moment.
  • BioPython - Tools for biological computation.
  • PyMongo - Python module needed for working with MongoDB.
  • pysam - Python module for reading and manipulating Samfiles.
  • bx-python - Python library and associated set of scripts to allow for rapid implementation of genome scale analyses.

For more detailed instructions on how to install the dependencies, pick your operating system from this list:

Installing with Pip

Pip is the preferred installation method on platforms other than Windows:

$ pip install capsid

To get a specific version of capsid:

$ pip install capsid==1.0

To upgrade using pip:

$ pip install capsid -U

Installing with easy_install

If you must install capsid using setuptools do:

$ easy_install capsid

To upgrade do:

$ easy_install -U capsid

Building from sources

If you'd rather install directly from the source, check out the latest source from github:

$ git clone git://github.com/capsid/capsid-pipeline.git capsid
$ cd capsid
$ python setup.py install --user   # installs to your home directory -- requires Python >= 2.6