Installation

Package Versioning

The hgvs package uses versions of the form major.minor.patch. Changes in patch level are for bug fixes only and will not have API changes. As hgvs is still a nascent project, API changes are possible even for minor (y) version changes. (As hgvs matures, will eventually adopt semantic versioning, in which breaking API changes will be restricted to major releases. We’re not ready for that yet.)

Version numbers for released code come directly from the repository tag. Therefore, PyPI version 0.1.2 corresponds exactly to the repository commit tagged as 0.1.2.

Users (i.e., non-developers) are encouraged to use the PyPI releases and to specify versions to stay within minor releases for API stability. For example, a line like:

hgvs>=0.4,<0.5

in setup.py or requirements.txt will use the latest patch level release (with bug fixes!) within the 0.4 series.

Supported Platforms

hgvs is developed primarily on Ubuntu systems (12.04 through 15.04) and has been reported to work on Mac. Other platforms and dependency versions are expected to work. Reports of successful operation on other platforms (and patches to enable this) are appreciated.

Install Prerequisites

hgvs currently requires PostgreSQL client libraries. (We are planning to switch to a REST interface and eliminate this dependency in the 0.5.0 release.) On Ubuntu, try:

apt-get install libpq-dev

On a Mac with homebrew:

brew install postgresql

Users are encouraged to use virtualenv (but this is optional):

$ sudo apt-get install python2.7 python2.7-dev libpq-dev mercurial virtualenvwrapper
$ mkvirtualenv hgvs-test

mkvirtualenv will automatically activate your virtualenv and usually change the prompt to indicate this.

Installing from PyPI

Ensure you have a current setuptools package:

$ pip install setuptools --upgrade

You’re now ready to install hgvs via pip:

$ pip install hgvs

hgvs will install dependencies automatically.

Installing from source

Note

Users (non-developers) should prefer the PyPI installation. There is no advantage to installing from source.

Fetch the source code using Mercurial:

$ hg clone https://bitbucket.org/biocommons/hgvs

Alternatively, see the Downloads section for tarballs and zipfiles.

Then:

$ cd hgvs
$ make install

Test your installation

Test your setup like this:

(hgvs-test)$ python
Python 2.7.5+ (default, Sep 19 2013, 13:48:49)
[GCC 4.8.1] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import hgvs.parser
>>> hgvs.parser.Parser().parse_hgvs_variant("NM_01234.5:c.12+3A>T")
SequenceVariant(ac=NM_01234.5, type=c, posedit=12+3A>T)

Local UTA Docker Instance

The public UTA is available without restrictions. However, some users may wish to install UTA locally for performance, isolation, or even Privacy Issues.

If you wish to install UTA locally, see the instructions on the available are described in the UTA bitbucket page.

Once the docker image is installed, you should set UTA_DB_URL to select it. A sample interaction:

$ docker run --name uta_20150827 -p 15032:5432 biocommons/uta:uta_20150827
$ export UTA_DB_URL=postgresql://anonymous@localhost:15032/uta/uta_20150827
$ python -c 'import hgvs.dataproviders.uta; print(hgvs.dataproviders.uta.connect().data_version());'
uta_20150827