Test drive overview¶
This overview provides step-by-step instructions for preparing a SeqsLab CLI environment, and managing data, tools, and jobs on the SeqsLab platform using the SeqsLab CLI.
From the Access information section of the marketplace test drive page, get the following information for platform access:
Azure AD account/password for the test drive
SeqsLab hostname: testdrive.seqslab.net
SeqsLab workspace: tdwestus2
The SeqsLab workspace is an environment providing the underlying storage, computation, and container registry service of the SeqsLab platform. The workspace is a required argument for most SeqsLab CLI commands.
SeqsLab CLI environment¶
Throughout the test drive, you will access the SeqsLab platform using the SeqsLab CLI. Open the terminal app, and use the following commands to prepare the SeqsLab CLI container environment.
Use the following command to launch SeqsLab CLI container.
docker run --rm --name cli \ -e PRIVATE_NAME="testdrive" \ -e WORKSPACE="tdwestus2" \ --privileged \ -it seqslabmain.azurecr.io/seqslab_cli
Once you’re inside the SeqsLab CLI container, use the following commands to set up the environment keyring and install the required packages.
dbus-run-session -- bash echo $RANDOM | gnome-keyring-daemon --unlock apt install zip wget -y
Next, sign in with the Azure AD account/password given in the Access information section. After you sign in successfully, you may be prompted with to set up the Multi-Factor Authentication (MFA) for the given Azure AD account. You can skip this process since the test drive will expire in two days.
seqslab auth signin -i
SeqsLab platform demonstration¶
After the SeqsLab CLI environment is prepared, the next step is to migrate existing data, tools, and workflow executions to the SeqsLab platform. This user guide uses a WGS-Germline-Snps-Indels workflow as an example, showing how to register the required reference/sample data, register the workflow, and eventually run the registered workflow based on the registered data.
The entire process can be broken down into three parts:
The test drive provides a demonstration of running the WGS-Germline-Snps-Indels workflow with a partially selected HG003 sample. However, the SeqsLab platform is more than capable of processing whole genome samples at scale, as well as adding sophisticated data parallelization and execution optimization. Find out more by reading this case study.