Detailed Installation:

Installing pypgen is very straightforward especially if you are familiar with installing python packages. Just follow the instructions below entering the appropriate commands in terminal.

Samtools and tabix

In OS X:

  1. Install Xcode or Xcode Command Line Tools. The CLI tools take up less space, but are an optional install under Xcode. Details on how to do this may be found in the homebrew documenation.

  2. Once xcode is installed, install the homebrew package installer:

    $ ruby -e "$(curl -fsSkL raw.github.com/mxcl/homebrew/go)"

  3. Then install samtools using homebrew:

    $ brew tap homebrew/science
$ brew install samtools
$ brew install tabix

While you’re at it you might want to use brew to install wget.

$ brew install wget

From source code (e.g., on linux):

  1. Download the latest version of samtools and tabix.

    # replace the ###version### with the appropriate version number (e.g., 0.2.6)

$ wget http://sourceforge.net/projects/samtools/files/tabix/tabix-###version###.tar.bz2
$ wget http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2

  2. Extract the tar.bz2 files

    tar jxf *.tar.bz2

  3. Then run make in each directory

  4. You’ll need to add these directories to your system profile files (e.g., .bashrc or .bash_profile)

# You can check that everything is working by opening a fresh shell. The commands samtools and tabix should now be available from anywhere in the file system.

Pip and Setuptools

  1. Unfortunately, pip doesn’t yet ‘play well’ with with setup.py, the script the automates the installation of python packages, as setup.py still relies on easy_install/setuptools to install dependancies. This means you’ll need to install setup tools. You’ll need to download the appropriate python .egg file. Then you can run it as an installation script.

    $ [sudo] sh setuptools-0.6c9-py2.7.egg

  2. Then you can use easy_install to install pip:

    $ [sudo] easy_install install -U pip

Pypgen

Pypgen can be installed from PyPi using pip or setuptools:

$ [sudo] pip install pypgen

or,

$ [sudo] easy_install -U pypgen

However, it’s recommended, at least in these early days of pypgen when I’m actively fixing bugs, to install it directly from the github repository:

$ [sudo] pip install -e git+https://github.com/ngcrawford/pypgen.git#egg=Package

This should complete your install.

UnitTests

UnitTests are in pygen/tests/tests.py

Pysam

NOTE: Pysam should automatically install when you install pypgen. These instructions are only necessary if you have problems with it.

Pysam is a bit of a finicky installation. The newest versions, in particular seem to have a lot of problems linking to their compiled cython libraries. With that in mind I recommend installing 0.6.

$ [sudo] pip install pysam==0.6

or,

$ [sudo] easy_install -U pysam==0.6

If that doesn’t work you’ll want to try installing it from source:

# replace the ###version### with the appropriate version number (e.g., 0.7.4)

$ wget http://pysam.googlecode.com/files/pysam-###version###.tar.gz
$ tar xzf pysam-###version###.tar.gz

then cd into the directory and run:

$ [sudo] python setup.py install

There is also a pysam google group that is a good source of information.