Follow these tutorials to learn how to use the BlobToolKit Pipeline.
Pipeline configuration
The Pipeline needs to be configured to match your local compute environment and to set parameters specific to your assembly and read data. These configuration options are set in a YAML format file before the Pipeline is run. Read more…
Running the Pipeline
The Pipeline is implemented as a Snakemake workflow that determines which jobs should be run to generate a complete BlobDir dataset based on the Pipeline configuration. The Pipeline can be run in the same way for both public and local assemblies, provided any local assembly and read files are available in the working directory. Read more…
Running the Pipeline on a cluster
As a Snakemake workflow, the Pipeline can be run on various types of cluster, however some variables may need to be set explicitly. In particular running the transferCompleted.smk workflow to validate generated BlobDirs and generate a set of static images requires Firefox and Selenium Webdriver and may need to be run under Singularity, using the BlobToolKit Docker image. Read more…