Installation guide

How to install

Make sure you have Python 3.6 or higher installed and in a terminal, run:

pip install molgenis-commander

If you also have Python 2.x installed on your machine (common for machines running MacOS), make sure to install the commander with the Python 3 version of pip:

pip3 install molgenis-commander

Upgrading

To upgrade to the newest version, run:

pip install --upgrade molgenis-commander

Or if you have both Python 2 and 3 installed, run:

pip3 install --upgrade molgenis-commander

Configuring

When you run the commander for the first time a configuration file will be created. If you need to run this step non-interactively (in a docker build step for example) you can set a special environment variable:

export MCMD_INSTALL_NON_INTERACTIVE=True
mcmd

This will make sure no questions are asked during installation and will create a configuration file with default values.

Troubleshooting

I've installed the commander with pip but when I run mcmd I get an error referencing Python 2.x

You've installed the commander with an old version of pip. Make sure your Python version is up to date (3.6 or higher) and that you've installed with the correct version of pip. (Make sure to uninstall your old version first with pip uninstall molgenis-commander).

I've installed the commander on Debian/Ubuntu but mcmd can't be found

pip installs commands in ~/.local/bin. Make sure that this folder is added to the path variable.