dna0ff/biograph

The BioGraph genomics analysis platform

BioGraph

This is the codebase for the BioGraph genomic analysis platform. It is free for academic use. See the LICENSE file for details.

Quick start

Download a pre-built binary from GitHub releases. Releases are statically built and should run on most recent Linux distributions.

In addition to the release, you will need a copy of the classifier model:

$ wget https://spiral-public.s3.us-west-2.amazonaws.com/models/biograph_model-7.0.0.ml

or

$ aws s3 cp s3://spiral-public/models/biograph_model-7.0.0.ml . --no-sign-request

You will also need a few common bioinformatics packages. To install them on Ubuntu:

$ sudo apt install -y vcftools tabix bcftools

BioGraph can also be run as a Docker container:

$ docker run spiralgenetics/biograph ...

Documentation

Full documentation available here

For other dependencies and full installation instructions, see the online installation docs.

Building the code

We recommend building on Ubuntu 18.04 or later. The following system dependencies are required:

$ apt-get install -y python3.6 python3.6-dev build-essential libbz2-dev libz-dev libcurl4-openssl-dev dh-autoreconf wamerican docker.io

You will also need a recent version of bazelisk. Download the binary for your architecture and save it to a file named bazel somewhere in your PATH.

Build and run all tests:

$ bazel test ... --config=manylinux2014

Create a release tarball:

$ bazel build -c opt --config=release //python/biograph:package