| Name | altocumulus JSON |
| Version |
2.3.0
JSON |
| download |
| home_page | |
| Summary | Command line utilities for workflows on Terra or Cromwell |
| upload_time | 2023-06-22 05:36:28 |
| maintainer | |
| docs_url | None |
| author | Bo Li, Joshua Gould, Yiming Yang |
| requires_python | >=3.8 |
| license | BSD 3-Clause License Copyright (c) 2019, klarman-cell-observatory All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
| keywords |
terra
cromwell
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
==============
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>`_.
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