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

Docker mount problem on MAC

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#328 5 comments 0 reactions 1 assignee Claimed by @michael-kotliar View on GitHub
OSX
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Python
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Description

Output from a step is saved to a folder which by default is not allowed to be mounted by Docker.
The folder is **/var/folders**. Default configuration includes: **/Users**, **/Volumes**, **/private**, **/tmp**. If add it manually in Docker preferences all works fine.

To run the test:
`cwl-runner --debug workflow.cwl job.yml`
Link to testing example:
https://github.com/michael-kotliar/cwl_sandbox/tree/master/mac_docker_fail

Part from the log:
```
[job copy_2] /var/folders/sd/41rg42_16q72_2yzl_vvgsbw0000gn/T/tmpuEpjSV$ docker \
run \
-i \
--volume=/var/folders/sd/41rg42_16q72_2yzl_vvgsbw0000gn/T/tmptNfjZl/./empty_copy.txt:/private/var/lib/cwl/stgcce3847f-a49b-4279-b1b1-0d5366ac8b4e/empty_copy.txt:ro \
--volume=/private/var/folders/sd/41rg42_16q72_2yzl_vvgsbw0000gn/T/tmpuEpjSV:/private/var/spool/cwl:rw \
--volume=/private/var/folders/sd/41rg42_16q72_2yzl_vvgsbw0000gn/T/tmpxbsJsT:/tmp:rw \
--workdir=/private/var/spool/cwl \
--read-only=true \
--user=501 \
--rm \
--env=TMPDIR=/tmp \
--env=HOME=/private/var/spool/cwl \
ubuntu \
cp \
/private/var/lib/cwl/stgcce3847f-a49b-4279-b1b1-0d5366ac8b4e/empty_copy.txt \
empty_copy_copy.txt
docker: Error response from daemon: Mounts denied: cker-for-mac/osxfs/#namespaces for more info.
.
l_vvgsbw0000gn/T/tmptNfjZl/./empty_copy.txt
is not shared from OS X and is not known to Docker.
You can configure shared paths from Docker -> Preferences... -> File Sharing.
See https://docs.docker.com/do.
ERRO[0000] error getting events from daemon: net/http: request canceled
```
Docker version:
```
Client:
Version: 17.03.0-ce
API version: 1.26
Go version: go1.7.5
Git commit: 60ccb22
Built: Thu Feb 23 10:40:59 2017
OS/Arch: darwin/amd64

Server:
Version: 17.03.0-ce
API version: 1.26 (minimum version 1.12)
Go version: go1.7.5
Git commit: 3a232c8
Built: Tue Feb 28 07:52:04 2017
OS/Arch: linux/amd64
Experimental: true
```
cwl-runner version: `1.0.20170224141733`

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