Getting started with msgen

msgen is a command-line client for the Microsoft Genomics service. You can follow the instructions below or try the Azure notebook tutorial here .


msgen is compatible with Python 2.7. We recommend using version 2.7.12 or later. msgen can be installed from PyPI.


sudo apt-get install -y build-essential libssl-dev libffi-dev libpython-dev python-dev python-pip
sudo pip install --upgrade --no-deps msgen
sudo pip install msgen


pip install --upgrade --no-deps msgen
pip install msgen

If you do not want to install msgen as a system-wide binary and modify system-wide python packages, use the --user flag with pip. In that case you will need to add ~/.local/bin to your path in Linux and %APPDATA%\Python in Windows.

Basic requirements

You can install these packages using pip, easy_install or through standard procedures. These dependencies will be automatically installed if using a package-based installation or The required versions of these dependent packages can be found in

Basic usage

After installing msgen, a simple command to check connectivity is:

Windows console
msgen list ^
  --api-url-base     <Genomics API URL> ^
  --subscription-key <Genomics account access key>
Unix console
msgen list \
  --api-url-base     <Genomics API URL> \
  --subscription-key <Genomics account access key>

Values for both these arguments can be found in Azure Portal, on the Access keys blade of your Genomics account.

You can get a full list of available commands and arguments by running msgen help, but generally you will need to provide at least a command, --api-url-base, and --access-key, where the command is one of the following:

list Returns a list of jobs you have submitted. For arguments, see msgen help list.
submit Submits a workflow request to the service. For arguments, see msgen help submit.
status Returns the status of the workflow specified by --workflow-id. See also msgen help status.
cancel Sends a request to cancel processing of the workflow specified by --workflow-id. See also msgen help cancel.

See also: How do I submit a pair of FASTQ files for processing? and How do I create a config file for msgen?