1. James Taylor
  2. bx-python


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bx-python / HowToInstall

Using easy_install

Most modern Python distributions include easy_install, so to install the latest revision:

easy_install https://bitbucket.org/james_taylor/bx-python/get/tip.tar.bz2

Using Anaconda python

Continuum IO provides an all in one scientific python stack and package management system called Anaconda. If you use Anaconda python, you can us the provided conda and binstar tools to install bx-python like so:

$ binstar search -t conda bx-python

Pick one of the available channels. I'll use bcbio in this example.

Using binstar api site https://api.binstar.org
Run 'binstar show <USER/PACKAGE>' to get more details:
     Name                      |  Version | Package Types   | Platforms
     ------------------------- |   ------ | --------------- | ---------------
     bcbio/bx-python           |    0.7.2 | conda           | linux-64, osx-64
                                          : Toolkit to enable rapid implementation of genome scale analyses.
     cgat/bx-python            |    0.7.2 | conda           | linux-64
     faircloth-lab/bx-python   |    0.7.1 | conda           | linux-64, osx-64
                                          : http://bitbucket.org/james_taylor/bx-python/wiki/Home
     lparsons/bx-python        |    0.7.1 | conda           | osx-64
                                          : http://bitbucket.org/james_taylor/bx-python/wiki/Home
Found 4 packages

Show the details of the package from the channel you choose, it will tell you how to install the package using conda

$ binstar show bcbio/bx-python
Using binstar api site https://api.binstar.org
Name:    bx-python
Summary: Toolkit to enable rapid implementation of genome scale analyses.
Access:  public
Package Types:  conda
   + 0.7.2

To install this package with conda run:
     conda install --channel https://conda.binstar.org/bcbio bx-python

Install the package

$ conda install --channel https://conda.binstar.org/bcbio bx-python


Checkout the current code from the SVN repository:

$ hg clone http://bitbucket.org/james_taylor/bx-python/ bx-python-central

This will checkout all the source code to the directory bx-python-central. Change to that directory:

$ cd bx-python-central

Then run the setup.py script. For example, to install under your home directory:

$ export PYTHONPATH=$HOME/lib/python
$ python setup.py install --home=$HOME

This will install package the code up in a python egg that is installed in $HOME/lib/python, and install wrapper scripts for all the tools into $HOME/bin.