Bug
CI tests fail with:
filesystem error: cannot create directories: Permission denied [//.config/OpenMS]
This affects all OpenMS tools (e.g., DecoyDatabase) running in the ghcr.io/openms/openms-tools-thirdparty:latest container.
Root cause
The container's $HOME resolves to / (root filesystem), and the new OpenMS version tries to create $HOME/.config/OpenMS on startup. The CI runner doesn't have write permission to /.config/.
Impact
All quantms CI tests that use OpenMS tools fail before reaching any pipeline logic. This blocks all PRs from passing CI (e.g., #690).
Reproduction
docker run ghcr.io/openms/openms-tools-thirdparty:latest DecoyDatabase --help
If $HOME is not set or is /, this will fail with the same permission error.
Suggested fix
Either:
- In the container: Set
HOME=/tmp or HOME=/home/openms in the Dockerfile so .config/OpenMS can be created
- In quantms: Set
HOME=/tmp as an environment variable in the Nextflow process definitions
- In OpenMS: Handle the case where
$HOME/.config is not writable (fall back to /tmp or skip config creation)
🤖 Generated with Claude Code
Bug
CI tests fail with:
This affects all OpenMS tools (e.g.,
DecoyDatabase) running in theghcr.io/openms/openms-tools-thirdparty:latestcontainer.Root cause
The container's
$HOMEresolves to/(root filesystem), and the new OpenMS version tries to create$HOME/.config/OpenMSon startup. The CI runner doesn't have write permission to/.config/.Impact
All quantms CI tests that use OpenMS tools fail before reaching any pipeline logic. This blocks all PRs from passing CI (e.g., #690).
Reproduction
If
$HOMEis not set or is/, this will fail with the same permission error.Suggested fix
Either:
HOME=/tmporHOME=/home/openmsin the Dockerfile so.config/OpenMScan be createdHOME=/tmpas an environment variable in the Nextflow process definitions$HOME/.configis not writable (fall back to/tmpor skip config creation)🤖 Generated with Claude Code