BradnerLab/pipeline — pull request #14 by jdimatteo (2014-05-31 20:38:43+00:00)
Title: Ease Installation

BamLiquidator is now easier to install and upgrade, leveraging apt-get install and pip. Installation instructions are at https://github.com/BradnerLab/pipeline/wiki/bamliquidator#Install .

`apt-get install bamliquidator` uses a debian package at the following ppa:

https://launchpad.net/~bradner-computation/+archive/pipeline

`pip install BamLiquidatorBatch` uses the python module here:

https://pypi.python.org/pypi/BamLiquidatorBatch/

Note that I re-organized a lot of the files for the creation of the debian package and the pip module. The debian package can be updated with the

Test plan:
# test the install instructions
# regression test bamliquidator: try a uniform bin run, try a region run, try running flattener, try running bamliquidator (not bamliquidator_batch) and confirm everything is found properly on the default search path (without having to provide a full path)
# test the upgrade and uninstall instructions

Note that ideally pip wouldn't be needed, but bamliquidator_batch.py uses bokeh and bokeh currently isn't able to be installed with apt-get. I could probably get the install to work without pip by packaging up bokeh and all of bokeh's dependiences but this would probably take in excess of 16 hours of time.