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"GA4GH Variation Representation (VR) reference implementation (https://github.com/ga4gh/vr-python/)"

Project description

Installation

1. Install vr-python

The following instructions are for Ubuntu 18.04+ and MacOS. vr-python is unlikely to work on Windows due to dependencies.

git clone --recurse-submodules https://github.com/ga4gh/vr-python.git
cd vr-python
python3.7 -m venv venv/3.7
source venv/3.7/bin/activate
pip install --upgrade pip setuptools
pip install -e .
pip install -e '.[dev,notebooks]'

(Python 3.5 and 3.6 should also work.)

2. Pull seqrepo data

Sequence data are required to normalize sequences and infer ga4gh sequence identifiers. The notebooks use SeqRepo. VR implementers may use SeqRepo or other data source.

Then, download seqrepo with:

sudo mkdir /usr/local/share/seqrepo
sudo chown $USER:$USER /usr/local/share/seqrepo
seqrepo pull

NOTE: This will download approximately 10GB of sequence data. See https://github.com/biocommons/biocommons.seqrepo/ for more information.

Running the Notebooks

Once installed as described above, type:

source venv/3.7/bin/activate
jupyter notebook --notebook-dir notebooks/

Security

A stand-alone security review has been performed on the specification itself. This implementation is offered as-is, and without any security guarantees. It will need an independent security review before it can be considered ready for use in security-critical applications. If you integrate this code into your application it is AT YOUR OWN RISK AND RESPONSIBILITY to arrange for a security audit.

Project details


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Files for ga4gh.vr, version 0.3.0
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