Pybamview

Browser-based application for viewing bam alignments



Note: PyBamView requires Python2.6.

easy installation

The easiest and preferred way to install PyBamView is using pip: 
pip install pybamview
This will install the latest stable PyBamView version listed in PyPi, and any missing libraries it depends on.

To use the "Export to PDF" feature or generate PDF snapshots using the snapbam tool, you will also need to install rsvg-convert: 
sudo apt-get install librsvg2-bin
(note that the "sudo apt-get" command is assuming you're using Ubuntu/Debian. If you're using a different system you will need to use that system's package manager.)

installing from source

requirements

First, make sure you have the required python packages installed: You can install these using easy_install: 
sudo easy_install Flask pyfasta pysam
If you want to use the "Download PDF" feature, you must have rsvg-convert installed (see above).

getting the source code

Obtain the source code by either:

building and installing

At the top of the PyBamView source directory, type: 
sudo python setup.py install
To make sure it was installed, type: 
pybamview --help
and ensure that the help message comes up. Then move on to the usage page to get started!