Installation

Prerequisites

svviz2 requires python version 3.3 or greater. Some of the packages that are installed by svviz2 also require a C compiler to be installed.

Additional, optional software:

• To perform tandem repeat detection, download tandem repeats finder, rename the binary to “trf” and move it into your $PATH
• To visualize the dotplots, the rpy2 package must be installed
• To convert visualizations to pdf format, either inkscape, rsvg-convert or (macOS only) webkitToPDF must be installed into your $PATH
• While svviz2 includes bwa internally, you may wish to install bwa mem in order to create reference index files

Installing into a virtual environment

The preferred method is to use pip to install svviz2 into a virtualenv:

python3 -m venv </path/to/svviz2_venv>
source </path/to/svviz2_venv/bin/activate>
pip3 install -U git+git://github.com/nspies/svviz2.git

An important note

svviz2 compiles against the installed version of pysam. If you update pysam, you very likely will need to reinstall svviz2.