Question: Does CWL have a search path for commadlinetools?
1
gravatar for thomas.e
20 months 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 • 541 views
ADD COMMENTlink modified 18 months ago by Michael R. Crusoe1.4k • written 20 months ago by thomas.e100
1
gravatar for Michael R. Crusoe
18 months ago by
Common Workflow Language project
Michael R. Crusoe1.4k 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 18 months ago by Michael R. Crusoe1.4k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1511 users visited in the last hour