Using the nfcore/tools docker image gets permission denied now
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bug
- Dominant language
- Python
- Stars
- 322
- Forks
- 255
- Avg merge
- 2d 3h
- Merged PRs (30d)
- 5
Description
Description of the bug
I'm using the docker image nfcore/tools to develop my pipelines and run schema build, but lately I am getting a permission denied issue when running the docker version.
Command used and terminal output
docker run -itv `pwd`:`pwd` -w `pwd` -u $(id -u):$(id -g) nfcore/tools
Unable to find image 'nfcore/tools:latest' locally
latest: Pulling from nfcore/tools
e1caac4eb9d2: Pull complete
51d1f07906b7: Pull complete
fe87ad6b112e: Pull complete
4d8ccb72bbad: Pull complete
8100581c78dd: Pull complete
7bfcabf371be: Pull complete
ffe7d43d52f3: Pull complete
4cf8394fe5e8: Pull complete
4a9ae2a4dd52: Pull complete
131ad79d069d: Pull complete
40be4339f485: Pull complete
70a19b5b9798: Pull complete
08030602159c: Pull complete
4f4fb700ef54: Pull complete
ec15d696e163: Pull complete
Digest: sha256:bf01e0890530576a543885d348642901e4b6252d9029108c8552fd6502e4b4de
Status: Downloaded newer image for nfcore/tools:latest
Could not create cache directory: /.cache/nfcore/cache_3.11.8
Traceback (most recent call last):
File "/usr/local/bin/nf-core", line 5, in <module>
from nf_core.__main__ import run_nf_core
File "/usr/local/lib/python3.11/site-packages/nf_core/__main__.py", line 26, in <module>
setup_nfcore_dir()
File "/usr/local/lib/python3.11/site-packages/nf_core/utils.py", line 340, in setup_nfcore_dir
os.makedirs(NFCORE_DIR)
File "<frozen os>", line 215, in makedirs
File "<frozen os>", line 225, in makedirs
PermissionError: [Errno 13] Permission denied: '/.config'
System information
Nextflow verison 23.10.1
Docker version 24.0.6, build ed223bc
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Reproduce the issue with the reported docker run command and inspect how the nfcore/tools image configures the container user, home, cache, and config paths. Use the traceback through /usr/local/lib/python3.11/site-packages/nf_core/main.py and utils.py as the entry point; done means the command works with the supplied host UID and GID without permission errors.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- docker, python
- Domain
- cli, devops
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100