Installation
############

VAMP
****
1. Download VAMP from https://bitbucket.org/lance_parsons/vamp/downloads
2. Unarchive into directory
    a. ``tar xzvf vamp-x.x.tar.gz``.
3. Install VAMP plus python dependencies: 
    a. ``cd vamp-x.x`` b. ``python setup.py install``
4. Build documentation (optional)
    a. ``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 <https://github.com/numpy/numpy/issues/2434>`_.
    * 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 <http://guide.macports.org/chunked/installing.xcode.html>`_
       for more information.



Third Party Tools
*****************
* Install `fastx_toolkit <http://hannonlab.cshl.edu/fastx_toolkit/>`_
* Install `Bedtools <http://code.google.com/p/bedtools/>`_
* Install `FastQC <http://www.bioinformatics.babraham.ac.uk/projects/fastqc/>`_
* Install `Bowtie <http://bowtie-bio.sourceforge.net/index.shtml>`_
* Install `SSAKE <http://www.bcgsc.ca/platform/bioinfo/software/ssake>`_
* (Optional) `Mugsy <http://mugsy.sourceforge.net/>`_
   * 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 <http://lagan.stanford.edu/>`_.


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 <http://biopython.org/>`_
* `Cython <http://http://http://cython.org/>`_
* `Numpy <http://http://www.scipy.org/>`_
* `bx-python <https://bitbucket.org/james_taylor/bx-python/>`_
* `cutadapt <http://code.google.com/p/cutadapt/>`_
* `pybedtools <http://pypi.python.org/pypi/pybedtools (at least v0.6)>`_
* `paired_sequence_utils <https://bitbucket.org/lance_parsons/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 <http://hannonlab.cshl.edu/fastx_toolkit/prefix_email.txt>`_
  for information on installing into an alternate location



Installation Tips
*****************
* `Using VAMP on on the Princeton Genomics cluster (cetus) </Genomics/grid/users/lparsons/mszpara/hsv_comparison/orig_output>`_