Closed rexwangcc closed 5 years ago
@barkasn Thanks for the feedback!
cromwell-tools submit: error: the following arguments are required: --inputs-file
makes me think that the installation on your py3 env might be failed, since it looks like a stale error message. raise_for_status()
for all of the CLI calls so that users can get the detailed message (user-friendly message) instead of just seeing 400 Client Error
. I will make the change and push the commits later.-h help has the --wdl-file and --inputs-file options on the same line, unlike everything else
it is because these are the only 2 required
arguments, others are optional to submit a workflowLGTM
Purpose
Please explain the purpose of this PR and include links to any GitHub issues that it fixes:
https://github.com/HumanCellAtlas/secondary-analysis/issues/503
Changes
Please list out what major changes were made in this PR to address the issue:
This PR fixes the CLI parameters, especially focused on the
/submit
command.Oracle's Java 8 installer seems to be broken now when downloading from the docker build context, switching to OpenJDK for future convenience!
For clarity, take out the
tenacity
retry policy from the library, so the/submit
command run and fail much faster, and the user-friendly message is shipped to users directly without being shadowed.Review Instructions
Please provide instructions about how should a reviewer test/verify the changes in this PR:
To test the cromwell-tools:
git checkout rex-fix-cromwell-tools-cli && git pull origin
pip install .
(It's recommended to use a virtualenv)It has been tested with:
cromwell-tools submit --url https://cromwell.mint-dev.broadinstitute.org --username *** --password *** -w pipelines/cellranger/cellranger.wdl --inputs_files pipelines/cellranger/test_inputs.json -o ../pipeline-tools/adapter_pipelines/cellranger/options.json
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Follow-up Discussions
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