Installation

Installation

Stable release

To install Biobank Tools, run this command in your terminal:

$ pip install biobank-tools
---> 100%
Successfully installed biobank-tools

This is the preferred method to install Biobank Tools, as it will always install the most recent stable release.

If you don't have pip installed, this Python installation guide can guide you through the process.

From source

The source for Biobank Tools can be downloaded from the Github repo.

You can either clone the public repository:

$ git clone git://github.com/altaf-ali/biobank-tools

Or download the tarball:

$ curl -OJL https://github.com/altaf-ali/biobank-tools/tarball/master

Once you have a copy of the source, you can install it with:

$ pip install .

Verify installation

Verify that Biobank Tools are installed correctly by running the biobank command.

$ biobank --help
Usage: biobank [OPTIONS] COMMAND [ARGS]...

Options:
  --install-completion  Install completion for the current shell.
  --show-completion     Show completion for the current shell, to copy it or
                        customize the installation.
  --help                Show this message and exit.

Commands:
  exclude  Exclude from biobank dataset.
  fields   Show dataset fields.
  import   Import biobank dataset.
  select   Select fields from a dataset.