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DataBiosphere / toil

A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python.
http://toil.ucsc-cgl.org/.
Apache License 2.0
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Toil utils do not work if AWS libraries are not installed #4952

Closed stxue1 closed 4 weeks ago

stxue1 commented 1 month ago

On the Slurm cluster, where Toil is installed with only the WDL extra:

stxue@mustard:/private/groups/patenlab/toil-dev/wdl-conformance-tests$ toil --version
/usr/lib/python3/dist-packages/paramiko/transport.py:236: CryptographyDeprecationWarning: Blowfish has been deprecated
  "class": algorithms.Blowfish,
Traceback (most recent call last):
  File "/private/home/stxue/.local/bin/toil", line 8, in <module>
    sys.exit(main())
  File "/private/home/stxue/.local/lib/python3.10/site-packages/toil/utils/toilMain.py", line 14, in main
    modules = loadModules()
  File "/private/home/stxue/.local/lib/python3.10/site-packages/toil/utils/toilMain.py", line 55, in loadModules
    from toil.utils import toilLaunchCluster  # noqa
  File "/private/home/stxue/.local/lib/python3.10/site-packages/toil/utils/toilLaunchCluster.py", line 22, in <module>
    from toil.lib.aws import build_tag_dict_from_env
  File "/private/home/stxue/.local/lib/python3.10/site-packages/toil/lib/aws/__init__.py", line 27, in <module>
    from mypy_boto3_s3.literals import BucketLocationConstraintType
ModuleNotFoundError: No module named 'mypy_boto3_s3'

┆Issue is synchronized with this Jira Story ┆Issue Number: TOIL-1580