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dnanexus-archive / dx-cwl

Import and run CWL workflows on DNAnexus (alpha)
Apache License 2.0
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Update code to work with latest cwltool #24

Open jsunny23 opened 6 years ago

jsunny23 commented 6 years ago

Cwltool made some updates to their code which makes it incompatible with dx-cwl. For instance, here where they changed the function name from defaultMakeTool to default_make_tool.

There are other places where the code is now broken, due to the cwltool changes.

skchronicles commented 5 years ago

Work-around

I am also obsveing the same error as well. If youpip install cwltool==1.0.20180225105849, an older release of cwltools from Feburary 28th 2018, it works!

I will also point out that is not the only problem. The README.mdtestfiles described here do not exist. I ended up using a test cwl file in this location: /path/to/git/repo/dx-cwl/tests/md5sum/md5sum.cwl

That being said, this command seemed to do the trick:

python dx-cwl compile-workflow tests/md5sum/md5sum.cwl  --token yourAUTHTOKEN --project yourPROJECTID

That being said, it may be time to update the install portion of the README.md.

Here are the steps I took for installation:

  1. virtualenv dxenv
  2. source dxenv/bin/activate
  3. pip install --upgrade pip
  4. pip install cwltool==1.0.20180225105849
  5. pip install PyYAML
  6. pip install dxpy

I am not sure why you are running that get-cwltool.sh script since you are already pip installing cwltool (seems unnecessary).