Installation

Install Prequisites

1. Bedtools

   1. Bedtools Installation Instructions

2. Cython

   1. pip install cython

Install VAMP

1. Download VAMP from https://bitbucket.org/szparalab/vamp/downloads

2. Unarchive into directory

   1. tar xzvf vamp-x.x.tar.gz.

3. Install VAMP (plus python dependencies):

   1. cd vamp-x.x
   2. python setup.py install

4. (optional) Build documentation

   1. cd docs
   2. make html

Notes

• OSX

  • XCode and Command Line Utilities must be installed prior to installing many of the required tools for VAMP. See the MacPorts XCode installtion instructions for more information.

Python Dependencies

By default, VAMP’s setup.py installs the required python dependencies listed below:

• Cython
• BioPython
• bx-python
• pybedtools
• argparse (only if Python version is < 2.7)

Non-root users

• If you are not root or just want to install this locally, one option is to use the --user parameter when installing. e.g.:

  pip install --user cython
  python setup.py install --user