permission denied in test folder
Opened this issue · 2 comments
jfear commented
Running the test locally with Docker is giving me a permission denied error when trying to write .snakemake
I have no name!@f2f073222e65:/opt/lcdb/test$ snakemake
Traceback (most recent call last):
File "/opt/conda/lib/python3.5/site-packages/snakemake/__init__.py", line 399, in snakemake
no_hooks=no_hooks)
File "/opt/conda/lib/python3.5/site-packages/snakemake/workflow.py", line 301, in execute
list_params_changes)
File "/opt/conda/lib/python3.5/site-packages/snakemake/persistence.py", line 24, in __init__
os.mkdir(self.path)
PermissionError: [Errno 13] Permission denied: '/opt/lcdb/test/.snakemake'
Maybe an OSX uid/gid thing?
jfear commented
Yep looks like a common issue:
For Example
Found if I just set uid:gid to 1000 it all seems to work.
docker run --rm -it -v $(pwd):/opt/lcdb -u 1000:1000 daler/smklo /bin/bash travis-test.sh
Unless you know a better way??
daler commented
Nope, I only learned of the -u
thing recently. I would either accept that I would have to chmod everything, or checkout a repo into /tmp and delete it later.
I think there's a lot of room for simplifying/wrapping/improving how the tests are run locally.