altocumulus 2.1.0

Command line utilities for running workflows

Command line utilities for running workflows on Terra or Cromwell including:

• Run a Terra method, and bulk add/delete methods on Terra.
• Submit WDL workflow jobs to a sever running Cromwell, as well as check jobs’ status, abort jobs, and get logs.
• Replace local file paths with remote Cloud (Google Cloud or Amazon AWS) bucket URIs, and automatically upload referenced files to Cloud buckets.
• Parse monitoring log files to determine optimal instance type and disk space.

Important tools used by Altocumulus:

• FireCloud Swagger
• Dockstore Swagger
• FireCloud Service Selector (FISS). In particular, fiss/firecloud/api.py.