toil: Latest toil no longer works with cactus

A cactus command that works in version 3.20 now gives this error with master (I’m using a newer toil to test kubernetes for cactus). It’s strange because Job._runner() has a defer argument in the source:

INFO:toil.worker:Redirecting logging to /data1/cactus/toil-6141c5d4-202b-4550-a160-4d43177be980-565d6e0ff41b452899bd1cc744672e86/tmpj9fnaA/worker_log.txt
Job ended: 'RunCactusPreprocessorThenProgressiveDown' kind-RunCactusPreprocessorThenProgressiveDown/instanceICGaXj
The job seems to have left a log file, indicating failure: 'RunCactusPreprocessorThenProgressiveDown' kind-RunCactusPreprocessorThenProgressiveDown/instanceICGaXj
INFO:toil:Running Toil version 3.21.0a1-81a543d0e1a8e6c299f22bb8e862d34097e1f0bc.
WARNING:toil.resource:'JTRES_612c0b9862883c5800042ea7ac702778' may exist, but is not yet referenced by the worker (KeyError from os.environ[]).
Traceback (most recent call last):
  File "/data1/cactus/toil-venv-master/local/lib/python2.7/site-packages/toil/worker.py", line 366, in workerScript
    job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer)
TypeError: _runner() got an unexpected keyword argument 'defer'
ERROR:toil.worker:Exiting the worker because of a failed job on host ip-172-31-26-21

This can be reproduced in a minute with these commands:

deactivate
git clone https://github.com/DataBiosphere/toil.git toil.master
git clone https://github.com/ComparativeGenomicsToolkit/cactus.git --recursive
cd cactus
virtualenv toil-venv-master
. toil-venv-master/bin/activate
pip install ../toil.master[all]
pip install .
toil clean jobStore ; cactus jobStore examples/evolverMammals.txt examples/evolverMammals.hal  --binariesMode docker --batchSystem singleMachine --workDir .

Doing the same thing with the last release runs okay

# Works with toil 3.20
deactivate
git clone https://github.com/DataBiosphere/toil.git toil.320
pushd toil.320 ;  git checkout cf34ca3416697f2abc816b2538f20ee29ba16932 ; popd
git clone https://github.com/ComparativeGenomicsToolkit/cactus.git --recursive
cd cactus
virtualenv toil-venv-320
. toil-venv-320/bin/activate
pip install ../toil.320[all]
pip install .
toil clean jobStore ; cactus jobStore examples/evolverMammals.txt examples/evolverMammals.hal  --binariesMode docker --batchSystem singleMachine --workDir .

┆Issue is synchronized with this Jira Task ┆Issue Number: TOIL-451