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This should close #4806 This is also related to #4807 The Dockerfile pulls from Github releases for now, but I will change it to a Debian mirror once the package...
This resolves #2739 This now properly carries through the status code of the debugged job. This will mean that a failing job in debug mode will retry according to `--retryCount`....
This will close #4827 ## Changelog Entry To be copied to the [draft changelog](https://github.com/DataBiosphere/toil/wiki/Draft-Changelog) by merger: * Add colored logging to Toil * Added a new option `--no-color` to disable...
Toil's logging can be very verbose and large sometimes. Colored logs might help with readability. I took a short glance at how MiniWDL does colored logs and it looks fairly...
Ex: on AWS where we have root permissions, we can install FUSE on the cluster. ┆Issue is synchronized with this [Jira Story](https://ucsc-cgl.atlassian.net/browse/TOIL-1506) ┆Issue Number: TOIL-1506
Ex: If there is FUSE implemented systemwide on Phoenix. FUSE in unprivileged mode may lack permissions to talk to the kernel directly, and have behavioral differences compared to running in...
`toil-wdl-runner` doesn't currently supporting call caching similar to MiniWDL. The restart system doesn't seem to be applicable as it stores data to input into future jobs rather than storing data...
If a WDL workflow has ```wdl runtime { memory: "1 GB" } ``` toil-wdl-runner will try to start a worker with 2147483648 bytes of memory. For example, on mesos/kubernetes, this...
The `TESBatchSystemTest.test_set_job_env` sometimes fails on CI https://ucsc-ci.com/databiosphere/toil/-/jobs/54265 ``` _____________________ TESBatchSystemTest.test_set_job_env ______________________ [gw0] linux -- Python 3.9.18 /builds/databiosphere/toil/venv/bin/python Traceback (most recent call last): File "/usr/lib/python3.9/unittest/case.py", line 59, in testPartExecutor yield File...
When Singularity is called with `--containall`, since it has to separate the PID namespaces, it tries to create its own proc filesystem as it can't take the existing proc from...