Question: Does CWL have a search path for commadlinetools?
1
gravatar for thomas.e
2.4 years ago by
thomas.e100
thomas.e100 wrote:

I'd like to setup a shared source for command line tools at our site and have people use them in individual workflows. For example:

mystep:
   run: mytool.cwl
etc

Is it part of the CWL spec that it can search a path, analogous to $PATH, $CLASSPATH or $PYTHONPATH? The documentation seems to imply that this should happen: http://www.commonwl.org/v1.0/CommandLineTool.html#Discovering_CWL_documents_on_a_local_filesystem but the reference implementation does not search these locations when looking for tools.

cwl • 705 views
ADD COMMENTlink modified 2.3 years ago by Michael R. Crusoe1.8k • written 2.4 years ago by thomas.e100
1
gravatar for Michael R. Crusoe
2.3 years ago by
Common Workflow Language project
Michael R. Crusoe1.8k wrote:

Hello thomas.e,

The paths from the spec (/usr/share/commonwl/, /usr/local/share/commonwl/, $XDG_DATA_HOME/commonwl/ (default equivalent to $HOME/.local/share/commonwl) should work, see https://github.com/common-workflow-language/cwltool/blob/master/cwltool/resolver.py#L15

Please file an issue on GitHub if this is not the case, thanks!

ADD COMMENTlink written 2.3 years ago by Michael R. Crusoe1.8k
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