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common-workflow-library / legacy

Deprecated
https://github.com/common-workflow-library/bio-cwl-tools
Apache License 2.0
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compile example command does not work #75

Open kblin opened 8 years ago

kblin commented 8 years ago

When trying to run the compile example, the provided command /cwl-runner --basedir ${PWD} compile1.cwl does not work (with cwltool, at least), even when disregarding the leading slash of the command.

Expected output is given in the README.md file, actual output is

$ cwltool --basedir ${PWD} compile1.cwl 
/home/kai/.virtualenvs/cwl/bin/cwltool 1.0.20160413143011
Tool file contains graph of multiple objects, must specify one of #compile, #link, #main

As the README.md file does not explain how to specify an object, a new user is a bit at a loss, and cwltool --help doesn't explain this either.

The README.md file should give $ cwltool --basedir ${PWD} compile1.cwl#main as the command to run.

mr-c commented 8 years ago

Hey @kblin , thank you for this.

You shouldn't need to use --basedir

kblin commented 8 years ago

Indeed I don't. I'll send you a pull request with a fix, then