diff --git a/docker/Dockerfile.general b/docker/Dockerfile.general index 0eda9d4..2813816 100644 --- a/docker/Dockerfile.general +++ b/docker/Dockerfile.general @@ -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"] @@ -36,6 +36,7 @@ RUN micromamba create -y -n ${ENV_NAME} \ psutil \ pyarrow \ fastparquet \ + biopython \ && micromamba clean --all --yes ENTRYPOINT ["micromamba", "run", "-n", "general"] diff --git a/docker/Dockerfile.ml b/docker/Dockerfile.gpu similarity index 87% rename from docker/Dockerfile.ml rename to docker/Dockerfile.gpu index eb2ce37..8839ed5 100644 --- a/docker/Dockerfile.ml +++ b/docker/Dockerfile.gpu @@ -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"] diff --git a/environments/README.md b/environments/README.md index 225bf87..5e5085c 100644 --- a/environments/README.md +++ b/environments/README.md @@ -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 diff --git a/environments/general.yml b/environments/general.yml index 67f5f38..ba0a8e7 100644 --- a/environments/general.yml +++ b/environments/general.yml @@ -1,4 +1,4 @@ -name: cobinet-general +name: domainbenchmark-general channels: - conda-forge - bioconda diff --git a/environments/ml.yml b/environments/ml.yml index d076bbf..28502e9 100644 --- a/environments/ml.yml +++ b/environments/ml.yml @@ -1,4 +1,4 @@ -name: cobinet-ml +name: domainbenchmark-gpu channels: - rapidsai - conda-forge diff --git a/modules/local/ddi_extraction/main.nf b/modules/local/ddi_extraction/main.nf index 0dd9bcd..cadbd29 100644 --- a/modules/local/ddi_extraction/main.nf +++ b/modules/local/ddi_extraction/main.nf @@ -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) diff --git a/modules/local/evaluation/main.nf b/modules/local/evaluation/main.nf index 6f38b6a..45555a3 100644 --- a/modules/local/evaluation/main.nf +++ b/modules/local/evaluation/main.nf @@ -8,7 +8,7 @@ process EVAL_ONE { label 'process_eval_scatter' conda "${projectDir}/environments/general.yml" - container "docker://konstantinpelz/cobinet-general:1.0.0" + container "docker://konstantinpelz/domainbenchmark-general:1.0.0" input: tuple val(meta), path(predictions) @@ -39,7 +39,7 @@ process EVALUATION { label 'process_eval' conda "${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) @@ -74,7 +74,7 @@ process COMBINE_EVAL { label 'process_eval' conda "${projectDir}/environments/general.yml" - container "docker://konstantinpelz/cobinet-general:1.0.0" + container "docker://konstantinpelz/domainbenchmark-general:1.0.0" input: // Every per-DB EVALUATION emits a dir literally named `evaluation/`, so diff --git a/modules/local/feature_extraction/main.nf b/modules/local/feature_extraction/main.nf index 839e334..de4496c 100644 --- a/modules/local/feature_extraction/main.nf +++ b/modules/local/feature_extraction/main.nf @@ -12,7 +12,7 @@ process FEATURE_EXTRACTION_ONE { label 'feature_extraction' conda "${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) @@ -66,7 +66,7 @@ process STAGE_FEATURE_DIR { label 'feature_stage' conda "${projectDir}/environments/general.yml" - container "docker://konstantinpelz/cobinet-general:1.0.0" + container "docker://konstantinpelz/domainbenchmark-general:1.0.0" input: tuple val(meta), path(h5_files) diff --git a/modules/local/graph_model/main.nf b/modules/local/graph_model/main.nf index 96e324b..88911cb 100644 --- a/modules/local/graph_model/main.nf +++ b/modules/local/graph_model/main.nf @@ -3,7 +3,7 @@ process GRAPH_MODEL { label 'process_high' conda "${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) diff --git a/modules/local/neural_network/main.nf b/modules/local/neural_network/main.nf index dd4ea16..4a43359 100644 --- a/modules/local/neural_network/main.nf +++ b/modules/local/neural_network/main.nf @@ -3,7 +3,7 @@ process NEURAL_NETWORK { label 'process_gpu' conda "${projectDir}/environments/ml.yml" - container "docker://konstantinpelz/cobinet-ml:1.0.0" + container "docker://konstantinpelz/domainbenchmark-gpu:1.0.0" input: tuple val(meta), path('DDI'), path('features/*'), path('config.json') @@ -48,7 +48,7 @@ process NEURAL_NETWORK_EVALUATION { errorStrategy 'ignore' conda "${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) diff --git a/modules/local/random_forest/main.nf b/modules/local/random_forest/main.nf index 48345e6..6b45970 100644 --- a/modules/local/random_forest/main.nf +++ b/modules/local/random_forest/main.nf @@ -3,7 +3,7 @@ process RANDOM_FOREST { label 'process_gpu' conda "${projectDir}/environments/ml.yml" - container "docker://konstantinpelz/cobinet-ml:1.0.0" + container "docker://konstantinpelz/domainbenchmark-gpu:1.0.0" input: tuple val(meta), path('DDI'), path('features/*'), path('config.json') @@ -45,7 +45,7 @@ process RANDOM_FOREST_EVALUATION { label 'process_long' conda "${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)