Installation

VAMP

1. Download VAMP from https://bitbucket.org/lance_parsons/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 b. python setup.py install

4. Build documentation (optional)

   1. cd docs b. make html

Known Issues

• ImportError: No module named numpy.distutils

  • This error occurs due to an issue when installing numpy as a setuptools (or distribute) dependency.
  • A workaround is to first install numpy, then install VAMP 1. pip install numpy==1.6.2 2. python setup.py install

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.

Third Party Tools

• Install fastx_toolkit

• Install Bedtools

• Install FastQC

• Install Bowtie

• Install SSAKE

• (Optional) Mugsy

  • Other alignment tools may be used to generate the required MAF or aligned fasta files. One option that works well for nearly complete genomes is LAGAN.

Configure third party tool locations

1. Copy makefiles/config.mk.template to makefiles/config.mk
2. Edit the locations of any of the required dependencies if they are not in your default PATH.

Python Dependencies

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

• BioPython
• Cython
• Numpy
• bx-python
• cutadapt
• pybedtools
• paired_sequence_utils

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 distribute as well as when using pip.
• See fastx_toolkit installation notes for information on installing into an alternate location

Installation Tips

• Using VAMP on on the Princeton Genomics cluster (cetus)