common-workflow-language / common-workflow-language/cwltool

attempts to write to /var/lib/cwl with docker hint but no docker installed

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#213 21 commenti 0 reazioni 0 assegnatari Vedi su GitHub
bug
Lingua principale
Python
Stelle
376
Fork
255
Merge medio
2g 7h
PR unite (30g)
12

Descrizione

On the 2 systems I have available to me (one of them Ubuntu 16), /var/lib is not user writable, so running the conformance test fails:

```
cwltest --tool cwltool --test=conformance_test_v1.0.yaml --junit-xml result.xml --basedir v1.0
Test [1/82] Got workflow error
Traceback (most recent call last):
File "/software/[...]/python-2.7.12/lib/python2.7/site-packages/cwltool/main.py", line 223, in single_job_executor
r.run(**kwargs)
File "/software/[...]/python-2.7.12/lib/python2.7/site-packages/cwltool/job.py", line 149, in run
stageFiles(self.pathmapper, os.symlink)
File "/software/[...]/python-2.7.12/lib/python2.7/site-packages/cwltool/process.py", line 176, in stageFiles
os.makedirs(os.path.dirname(p.target), 0755)
File "/software/[...]/python-2.7.12/lib/python2.7/os.py", line 150, in makedirs
makedirs(head, mode)
File "/software/[...]/python-2.7.12/lib/python2.7/os.py", line 157, in makedirs
mkdir(name, mode)
OSError: [Errno 13] Permission denied: '/var/lib/cwl'
```

Is this expected, and will I hit the same problem trying to run "real" cwl scripts? That is, is sudo required to use cwltool fully?

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