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I run in windows cygwin and have the following problem. how do i increase the workspace and any other error that you can see in the log file.
$ ./pgap.py -r -o k_pneu_results k_pneu.yaml
PGAP ver…
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## Description
When using `setup.cfg` as defined in https://docs.pytest.org/en/stable/reference/customize.html#setup-cfg, the parsing of arguments `log_format` and `log_date_format` (as in below ex…
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https://github.com/jshint/jshint/blob/master/src/jshint.js
> The Software shall be used for Good, not Evil.
https://wiki.debian.org/qa.debian.org/jsonevil
Might have to remove this in the meant…
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(to be done after the issues in https://github.com/common-workflow-lab/wdl-cwl-translator/milestone/1 are done)
For processing of the WDL `command` section and the functions inside the WDL Expressi…
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How do I run this pipeline from my CLI?
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toil version: `5.4.0a1`
cwltool version: `3.0.20201203173111`
Could anyone shed some light on the following error:
```
[2021-08-10T15:54:28-0400] [MainThread] [D] [toil.deferred] Running orphaned d…
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When running `toil-cwl-runner` with a DockerRequirement the docker command uses `--net=none` instead of `--net=host` or not specifying it at all.
I've found this can causes some java tool crash.
Thi…
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The `setup.py` `install_requires` for `reana-client` `v0.7.5` distributed on PyPI are creating dependency conflicts that `pip`'s dependency resolver is struggling to resolve
https://github.com/rean…
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## Bug Report
### Expected behaviour
pip installation instructions with python 3 should probably say pip3 to be explicit.
should mention that cwltool may not work unless you log out and log back in…
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**Describe the bug**
I am using build 5742, and am able to successfully run PGAP on the test genome MG37. However, my attempts to run PGAP on Brucella ovis chromosome 1 or B. ovis chomosome 2 end in …