Stuck on an issue?

Lightrun Answers was designed to reduce the constant googling that comes with debugging 3rd party libraries. It collects links to all the places you might be looking at while hunting down a tough bug.

And, if you’re still stuck at the end, we’re happy to hop on a call to see how we can help out.

cwltool fails in git bash

See original GitHub issue

reporting this for @am-cornelis trying to run cwltool in git bash (on Windows) fails when trying to create a symlink.

I’m pasting below the extensive bug report she sent me:

At the ELIXIR All Hands - CWL workshop, I came across the following error message, which you wanted to hear about.

I was running the cwl-runner on windows using git bash:

$ cwl-runner helloworld.cwl input.yaml
C:\Apps\Python27\Scripts\cwl-runner 1.0.20170309164828
Resolved 'helloworld.cwl' to
'file:///C:/src/play/cwl-workshop/helloworld.cwl'
Got workflow error
Traceback (most recent call last):
  File "c:\apps\python27\lib\site-packages\cwltool\main.py", line 230,
in single_job_executor
    r.run(**kwargs)
  File "c:\apps\python27\lib\site-packages\cwltool\job.py", line 213, in run
    stageFiles(self.pathmapper, os.symlink, ignoreWritable=True)
AttributeError: 'module' object has no attribute 'symlink'
Workflow error, try again with --debug for more information:
'module' object has no attribute 'symlink'

This is my setup:

Windows 10 Pro, with Git Bash (2.7.0)

$ python --version
Python 2.7.11

$ pip --version
pip 7.1.2 from c:\apps\python27\lib\site-packages (python 2.7)

$ cwl-runner --version
C:\Apps\Python27\Scripts\cwl-runner 1.0.20170309164828

Cheers, Amélie

Issue Analytics

State:
Created 6 years ago
Comments:6 (4 by maintainers)

Top GitHub Comments

1reaction

kapilkd13commented, Jul 24, 2017

Hi @xamgore @am-cornelis We have made cwltool compatible with windows with the latest release. You can try it by updating your cwltool. Just to clarify, you won’t need to use git bash, command prompt would work 😃 . Documentation on windows usage is currently in this PR https://github.com/common-workflow-language/cwltool/pull/486

0reactions

manu-chromacommented, Aug 4, 2017

I’m closing this issue now – @hmenager @am-cornelis.

@kapilkd13 has already provided all the relevant details.

Top Results From Across the Web

running "git log" results in an error saying "less: -c: line 0

In my understanding, the output maybe refers to an shell script, when executing git log , the srcipt will be executed(maybe it's named...

Introduction to Workflows with Common Workflow Language

This tutorial requires three pieces of software to run and visualize the workflows: Docker, cwltool, and graphviz. Please follow instructions for your OS...

Error collecting output for parameter 'concat_meta_ms' (#4) · Issues ...

I got an error when processing Target: [1;30mERROR[0m [31m[job ms_concat] Job ... git checkout concat_meta_ms ... and then from its shell run cwltool,...

CWL error when using OxoG: Tool definition failed validation

problems running command: cwltool --non-strict --print-pre /tmp/1502088182535-0/oxog_varbam_annotate_wf.cwl stderr for command:

Repeat mapping

PuTTY, git bash). ... You can verify installation with: cwltool --help ... ERROR '$TOOL' not found: [Errno 2] No such file or directory: ......