altocumulus

============== Altocumulus

|PyPI| |Python| |License| |Docs|

.. |PyPI| image:: https://img.shields.io/pypi/v/altocumulus.svg :target: https://pypi.org/project/altocumulus .. |Python| image:: https://img.shields.io/pypi/pyversions/altocumulus :target: https://pypi.org/project/altocumulus .. |License| image:: https://img.shields.io/github/license/lilab-bcb/altocumulus :target: https://github.com/lilab-bcb/altocumulus/blob/master/LICENSE .. |Docs| image:: https://readthedocs.org/projects/altocumulus/badge/?version=latest :target: https://altocumulus.readthedocs.io

Command line utilities for running workflows on Terra <https://app.terra.bio>_ or Cromwell <https://cromwell.readthedocs.io>_ 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 <https://api.firecloud.org/>_
• Dockstore Swagger <https://dockstore.org/api/static/swagger-ui/index.html>_
• FireCloud Service Selector <https://github.com/broadinstitute/fiss>_ (FISS). In particular, fiss/firecloud/api.py <https://github.com/broadinstitute/fiss/blob/master/firecloud/api.py>_.