As mentioned elsewhere, https://github.com/common-workflow-language/cwltool/releases/tag/1.0.20191225192155 has been released with common-workflow-language/cwltool#1228 incorporated

The call to cwltool's load_tool.validate_document() method in https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/tool_util/cwl/schema.py#L42 was broken in commit common-workflow-language/cwltool@526f36f
Any help on a fix for that in galaxy-tool-util would be appreciated!

It is almost certainly fixed in the CWL branch of Galaxy already. I'll see what I can do.

https://github.com/galaxyproject/galaxy/compare/dev...common-workflow-language:cwl-1.0-rebase-20191231?expand=1#diff-9f5ed620db2b8c1f6fbb4d19cfb8a33d

Update: I think I meant https://github.com/common-workflow-language/galaxy/blob/e18fdd8da1ffe6c48fb4f5f22750f97abf8a2669/lib/galaxy/tool_util/cwl/schema.py

Hmm, somethings hanging in the full test suite, possibly test_local_conda_dependencies_version. I have no idea what is going on there.

This process 30877 s008 S+ 0:00.00 /bin/bash -e /Users/john/miniconda3/conda-bld/fleeqtk_1579101053099/test_tmp/run_test.sh seems to hang locally. I don't know if this always hung on Macs though.

Replacing the fleeqtk test with 'true' ... https://github.com/jmchilton/planemo/runs/391338751 ... lets see what happens.

The original seqtk recipe now has an additional patch ... perhaps that might be needed now too? https://github.com/bioconda/bioconda-recipes/blob/master/recipes/seqtk/meta.yaml#L12

Might be better easier just patch fleeqtk if we think this is the problem.

I also see the fleeqtk seq hang during conda build locally. I've pushed a commit which changes the test a bit, seems to work for me.

Yeah, the additional patch doesn't make it a great example anymore. The original seqtk recipe builds fine, so let's patch fleeqtk

If this doesn't fix things - lets cherry-pick this ( jmchilton@371f3d2 ) - I think that should build a new fleeqtk 1.4 with the patch applied.

That was a long journey - thanks for the effort all!