v2.0.0: docker build fails with KeyError 'dseg_dentate' in import_template_dseg_dentate (--use-template-seg)
- Dominant language
- Python
- Stars
- 69
- Forks
- 24
- PR merge metrics
- No merged PRs in 30d
Description
Building v2.0.0 (ffb1e85) via podman on macOS (apple silicon; using the `podman-rootful` vm template from lima).
Build fails at the 9th `/app/entrypoint.sh` call in the second `RUN` block. The prior 8 calls ran successfully.
Dockerfile line:
```shell
/app/entrypoint.sh hippunfold test_data/bids_T1w test_out participant --modality T1w --use-template-seg --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs --conda-frontend mamba
```
Traceback:
```
Building DAG of jobs...
InputFunctionException in rule import_template_dseg_dentate in file "/src/hippunfold/workflow/rules/download.smk", line 142:
Error:
KeyError: 'dseg_dentate'
Wildcards:
subject=001
hemi=L
Traceback:
File "/src/hippunfold/workflow/rules/download.smk", line 149, in (rule import_template_dseg_dentate, line 232, /src/hippunfold/workflow/rules/download.smk)
Error: building at STEP "RUN set -e && /app/entrypoint.sh hippunfold test_data/bids_singleT2w test_out participant --modality T2w --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs --conda-frontend mamba && /app/entrypoint.sh hippunfold test_data/bids_multiT2w test_out participant --modality T2w --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs --conda-frontend mamba && /app/entrypoint.sh hippunfold test_data/bids_T1w test_out participant --modality T1w --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs --conda-frontend mamba && /app/entrypoint.sh hippunfold test_data/bids_hippb500 test_out participant --modality hippb500 --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs --conda-frontend mamba && /app/entrypoint.sh hippunfold test_data/bids_singleT2w_longitudinal test_out participant --modality T2w --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs --conda-frontend mamba && /app/entrypoint.sh hippunfold test_data/bids_dsegtissue test_out participant --modality dsegtissue --derivatives test_data/bids_dsegtissue --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs --conda-frontend mamba && /app/entrypoint.sh hippunfold test_data/bids_singleT2w test_out participant --modality T2w --t1_reg_template --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs --conda-frontend mamba && /app/entrypoint.sh hippunfold test_data/bids_singleT2w test_out participant --modality T2w --output_space T1w --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs --conda-frontend mamba && /app/entrypoint.sh hippunfold test_data/bids_T1w test_out participant --modality T1w --use-template-seg --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs --conda-frontend mamba && /app/entrypoint.sh hippunfold test_data/bids_singleT2w test_out participant --modality T2w --generate-myelin-map --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs --conda-frontend mamba && /app/entrypoint.sh hippunfold test_data/bids_dsegtissue test_out group_create_atlas --modality dsegtissue --derivatives test_data/bids_dsegtissue --new-atlas-name mytestatlas --new_atlas_subfields_from native --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs --conda-frontend mamba && rm -rf /root/.cache": while running runtime: exit status 1
```
Contributor guide
No contributing guide indexed for this repository
Research direction
Reproduce the failing Dockerfile RUN sequence, then inspect workflow/rules/download.smk around lines 142 and 149 and the /app/entrypoint.sh invocation using --use-template-seg. Trace why the dseg_dentate key is missing for subject 001 and hemisphere L; done means the v2.0.0 build completes that command without the KeyError.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- docker, python
- Domain
- build-system, devops
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100