1. Installation

1.1. Prerequisites

• python 3.4+
• Pillow (Python Imaging Library) (2.0.0+)
• pysam (0.11.2.2+)
• pyfaidx (0.5.3.1+)
• pytabix (0.0.2+)

1.2. Install with pypi

To install BamSnap with pip run:

$ pip install bamsnap
$ bamsnap

1.3. Install from source

$ git clone https://github.com/parklab/bamsnap
$ cd bamsnap
$ python setup.py install
$ bamsnap

1.4. Install from docker hub

$ docker pull danielmsk/bamsnap
$ docker images

REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE
danielmsk/bamsnap   latest              f9f6e61c7673        2 hours ago         997MB

$ docker run --rm -it -v /local_directory_path:/directory_path_in_image \
  danielmsk/bamsnap bamsnap \
    -bam /directory_path_in_image/test.bam \
    -pos 1:7364529 \
    -out /directory_path_in_image/test.png

The docker image can be pulled from the docker hub site (https://hub.docker.com/r/danielmsk/bamsnap). When you are using bamsnap from docker image, you should assign the local directory path (volume) and the image direcotry path (volume) using -v option.