This is the codebase for the BioGraph genomic analysis platform. It is free for academic use. See the LICENSE file for details.
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 ...
Full documentation available here
For other dependencies and full installation instructions, see the online installation docs.
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