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Merged
PelzKo merged 1 commit into from
Aug 5, 2026
Merged

changed docker container naming scheme #2

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5 changes: 3 additions & 2 deletions docker/Dockerfile.general
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Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
FROM mambaorg/micromamba:1.5.10

# Build/tag as konstantinpelz/cobinet-general:1.0.0 — synced with environments/general.yml
# Build/tag as konstantinpelz/domainbenchmark-general:1.0.0 — synced with environments/general.yml
LABEL org.opencontainers.image.source="https://github.com/daisybio/domainbenchmark"
LABEL org.opencontainers.image.version="1.0.0"
LABEL org.opencontainers.image.description="cobinet general CPU container (multiqc, scikit-learn, networkx, h5py)"
LABEL org.opencontainers.image.description="general CPU container (multiqc, scikit-learn, networkx, h5py)"

SHELL ["/bin/bash", "-o", "pipefail", "-c"]

Expand Down Expand Up @@ -36,6 +36,7 @@ RUN micromamba create -y -n ${ENV_NAME} \
psutil \
pyarrow \
fastparquet \
biopython \
&& micromamba clean --all --yes

ENTRYPOINT ["micromamba", "run", "-n", "general"]
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4 changes: 2 additions & 2 deletions docker/Dockerfile.ml → docker/Dockerfile.gpu
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@@ -1,9 +1,9 @@
FROM mambaorg/micromamba:1.5.10

# Build/tag as konstantinpelz/cobinet-ml:1.0.0 — synced with environments/ml.yml
# Build/tag as konstantinpelz/domainbenchmark-gpu:1.0.0 — synced with environments/ml.yml
LABEL org.opencontainers.image.source="https://github.com/daisybio/domainbenchmark"
LABEL org.opencontainers.image.version="1.0.0"
LABEL org.opencontainers.image.description="cobinet GPU container (CUDA 12.8, cuML 26.02, torch 2.7, skorch)"
LABEL org.opencontainers.image.description="GPU container (CUDA 12.8, cuML 26.02, torch 2.7, skorch)"

SHELL ["/bin/bash", "-o", "pipefail", "-c"]

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4 changes: 2 additions & 2 deletions environments/README.md
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Expand Up @@ -4,8 +4,8 @@ Two environments are the single source of truth for runtime dependencies.

| File | Purpose | Container tag |
|---------------|----------------------------------|-------------------------------------|
| `general.yml` | CPU env (eval, graph models, IO) | `konstantinpelz/cobinet-general:1.0.0` |
| `ml.yml` | GPU env (ML, RF, cuML, torch) | `konstantinpelz/cobinet-ml:1.0.0` |
| `general.yml` | CPU env (eval, graph models, IO) | `konstantinpelz/domainbenchmark-general:1.0.0` |
| `ml.yml` | GPU env (ML, RF, cuML, torch) | `konstantinpelz/domainbenchmark-gpu:1.0.0` |

The `docker/Dockerfile.base` and `docker/Dockerfile.ml` images mirror these
files. When pinning a package version here, update the corresponding line in
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2 changes: 1 addition & 1 deletion environments/general.yml
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@@ -1,4 +1,4 @@
name: cobinet-general
name: domainbenchmark-general
channels:
- conda-forge
- bioconda
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2 changes: 1 addition & 1 deletion environments/ml.yml
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@@ -1,4 +1,4 @@
name: cobinet-ml
name: domainbenchmark-gpu
channels:
- rapidsai
- conda-forge
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2 changes: 1 addition & 1 deletion modules/local/ddi_extraction/main.nf
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Expand Up @@ -3,7 +3,7 @@ process DDI_EXTRACTION {
label 'process_low'

conda "${projectDir}/environments/general.yml"
container "docker://konstantinpelz/cobinet-general:1.0.0"
container "docker://konstantinpelz/domainbenchmark-general:1.0.0"

input:
tuple val(meta), path(database_dir)
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6 changes: 3 additions & 3 deletions modules/local/evaluation/main.nf
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Expand Up @@ -8,7 +8,7 @@ process EVAL_ONE {
label 'process_eval_scatter'

conda "${projectDir}/environments/general.yml"
container "docker://konstantinpelz/cobinet-general:1.0.0"
container "docker://konstantinpelz/domainbenchmark-general:1.0.0"

input:
tuple val(meta), path(predictions)
Expand Down Expand Up @@ -39,7 +39,7 @@ process EVALUATION {
label 'process_eval'

conda "${projectDir}/environments/general.yml"
container "docker://konstantinpelz/cobinet-general:1.0.0"
container "docker://konstantinpelz/domainbenchmark-general:1.0.0"

input:
tuple val(meta), path(database), path(per_model_jsons), val(old_report)
Expand Down Expand Up @@ -74,7 +74,7 @@ process COMBINE_EVAL {
label 'process_eval'

conda "${projectDir}/environments/general.yml"
container "docker://konstantinpelz/cobinet-general:1.0.0"
container "docker://konstantinpelz/domainbenchmark-general:1.0.0"

input:
// Every per-DB EVALUATION emits a dir literally named `evaluation/`, so
Expand Down
4 changes: 2 additions & 2 deletions modules/local/feature_extraction/main.nf
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Expand Up @@ -12,7 +12,7 @@ process FEATURE_EXTRACTION_ONE {
label 'feature_extraction'

conda "${projectDir}/environments/general.yml"
container "docker://konstantinpelz/cobinet-general:1.0.0"
container "docker://konstantinpelz/domainbenchmark-general:1.0.0"

input:
tuple val(meta), path(database_dir)
Expand Down Expand Up @@ -66,7 +66,7 @@ process STAGE_FEATURE_DIR {
label 'feature_stage'

conda "${projectDir}/environments/general.yml"
container "docker://konstantinpelz/cobinet-general:1.0.0"
container "docker://konstantinpelz/domainbenchmark-general:1.0.0"

input:
tuple val(meta), path(h5_files)
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2 changes: 1 addition & 1 deletion modules/local/graph_model/main.nf
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Expand Up @@ -3,7 +3,7 @@ process GRAPH_MODEL {
label 'process_high'

conda "${projectDir}/environments/general.yml"
container "docker://konstantinpelz/cobinet-general:1.0.0"
container "docker://konstantinpelz/domainbenchmark-general:1.0.0"

input:
tuple val(meta), path(database), path(model_json)
Expand Down
4 changes: 2 additions & 2 deletions modules/local/neural_network/main.nf
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Expand Up @@ -3,7 +3,7 @@ process NEURAL_NETWORK {
label 'process_gpu'

conda "${projectDir}/environments/ml.yml"
container "docker://konstantinpelz/cobinet-ml:1.0.0"
container "docker://konstantinpelz/domainbenchmark-gpu:1.0.0"

input:
tuple val(meta), path('DDI'), path('features/*'), path('config.json')
Expand Down Expand Up @@ -48,7 +48,7 @@ process NEURAL_NETWORK_EVALUATION {
errorStrategy 'ignore'

conda "${projectDir}/environments/ml.yml"
container "docker://konstantinpelz/cobinet-ml:1.0.0"
container "docker://konstantinpelz/domainbenchmark-gpu:1.0.0"

input:
tuple val(meta), path('DDI'), path('features/*'), path('config.json'), path(prev_results)
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4 changes: 2 additions & 2 deletions modules/local/random_forest/main.nf
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Expand Up @@ -3,7 +3,7 @@ process RANDOM_FOREST {
label 'process_gpu'

conda "${projectDir}/environments/ml.yml"
container "docker://konstantinpelz/cobinet-ml:1.0.0"
container "docker://konstantinpelz/domainbenchmark-gpu:1.0.0"

input:
tuple val(meta), path('DDI'), path('features/*'), path('config.json')
Expand Down Expand Up @@ -45,7 +45,7 @@ process RANDOM_FOREST_EVALUATION {
label 'process_long'

conda "${projectDir}/environments/ml.yml"
container "docker://konstantinpelz/cobinet-ml:1.0.0"
container "docker://konstantinpelz/domainbenchmark-gpu:1.0.0"

input:
tuple val(meta), path('DDI'), path('features/*'), path('config.json'), path(prev_results)
Expand Down
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