Microsoft Genomics Command-line Client
msgen is a command-line client for the Microsoft Genomics service. You can find more detailed documentation for it here: https://msgen.readthedocs.io/
- Submitting multiple FASTQ or multiple BAM files.
- Filtering options for the list command.
- Range limiting options for the list command.
- Export to CSV of the list command output.
- Bug fixes!
This version of msgen also introduces user interface changes compared to version 0.6.*. If you would like to keep using an older version, you can downgrade back to 0.6.15 by running the following command:
pip install msgen==0.6.15
Otherwise, you may want to scroll down to Breaking changes.
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.
You can install these packages using pip, easy_install or through standard setup.py procedures. These dependencies will be automatically installed if using a package-based installation or setup.py. The required versions of these dependent packages can be found in setup.py.
After installing msgen, a simple command to check connectivity is:
REM Windows console msgen list ^ --api-url-base <Genomics API URL> ^ --access-key <Genomics account access key>
# Unix console msgen list \ --api-url-base <Genomics API URL> \ --access-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.|
Breaking changes from 0.6.15
Previously, the operation you wanted to invoke was a parameter to the -command option. Now, the desired command directly follows the program name, msgen. Below is a table comparing invocations of msgen 0.6.* and 0.7.* for cases when a configuration file is not used.
|msgen 0.6.* (without config)||msgen 0.7.* (without config)|
|msgen -command submit …||msgen submit …|
|msgen -command list …||msgen list …|
|msgen -command getstatus …||msgen status …|
|msgen -command cancel …||msgen cancel …|
Commands cannot be specified in the configuration file anymore and will be ignored if mentioned there. Below is a table comparing invocations between msgen 0.6.* and 0.7.* for cases when a configuration file is used.
|Command in the config file||msgen 0.6.* (with command in config)||msgen 0.7.* (with config)|
|command: submit||msgen -f config.txt …||msgen submit -f config.txt …|
|command: list||msgen -f config.txt …||msgen list -f config.txt …|
|command: getstatus||msgen -f config.txt …||msgen status -f config.txt …|
|command: cancel||msgen -f config.txt …||msgen cancel -f config.txt …|
Specifying other arguments
Using the command line
If you provide at least some required information via the command line arguments when interacting with the Microsoft Genomics service, you will need to update your command invocation. All arguments are now provided either in the short format like -k or in the long format like --access-key. Note that arguments in the long format start with a double dash and that underscores between words are replaced with dashes. Below is a table listing some of the submit arguments to illustrate this difference between msgen 0.6.* and 0.7.*.
|msgen 0.6.*||msgen 0.7.*|
Using the configuration file
There are no changes here, apart from the fact that the command is going to be ignored and will need to be provided on the command line. Your old configuration file can be re-used for all commands you want to use it with.
Release history Release notifications
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
|Filename, size & hash SHA256 hash help||File type||Python version||Upload date|
|msgen-0.7.4-py2-none-any.whl (28.7 kB) Copy SHA256 hash SHA256||Wheel||py2||Mar 6, 2018|
|msgen-0.7.4.tar.gz (23.6 kB) Copy SHA256 hash SHA256||Source||None||Mar 6, 2018|