Apptainer def files, env input yamls for build.

README instructions for build and run.
PMBio · Feb 3, 2025 · 5ded441 · 5ded441
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diff --git a/containers/README.md b/containers/README.md
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+# Build Container
+apptainer build deeprvat_preprocessing.sif apptainer_deeprvat_preprocessing.def
+apptainer build deeprvat.sif apptainer_deeprvat.def
+
+NOTE: deeprvat image ~= 5 GB, deeprvat_preprocessing image ~= 1 GB
+
+# Verify Working Image
+apptainer exec deeprvat_preprocessing.sif pip list | grep "deeprvat"
+
+# Run Preprocessing
+cd ./my_exp_dir
+    .
+    ├── data
+    │   └── vcf
+    │       ├── test_vcf_data_c21_b1.vcf.gz
+    │       └── test_vcf_data_c22_b1.vcf.gz
+    ├── deeprvat_preprocess_config.yaml
+    ├── deeprvat_preprocessing.sif
+    └── vcf_files_list.txt
+
+
+[~/my_exp_dir]$ apptainer run deeprvat_preprocessing.sif snakemake -j 1 --snakefile /opt/deeprvat/pipelines/preprocess_no_qc.snakefile --configfile deeprvat_preprocess_config.yaml --ri -n
+
+
+# Run Training + Association Testing
+cd ./my_exp_dir
+    .
+    ├── annotations.parquet
+    ├── baseline_results
+    │   ├── Apolipoprotein_A
+    │   │   ├── missense
+    │   │   │   ├── burden
+    │   │   │   │   └── eval
+    │   │   │   │       └── burden_associations.parquet
+    │   │   │   └── skat
+    │   │   │       └── eval
+    │   │   │           └── burden_associations.parquet
+    │   │   └── plof
+    │   │       ├── burden
+    │   │       │   └── eval
+    │   │       │       └── burden_associations.parquet
+    │   │       └── skat
+    │   │           └── eval
+    │   │               └── burden_associations.parquet
+    │   ├── Calcium
+    │   │   ├── missense
+    │   │   │   ├── burden
+    │   │   │   │   └── eval
+    │   │   │   │       └── burden_associations.parquet
+    │   │   │   └── skat
+    │   │   │       └── eval
+    │   │   │           └── burden_associations.parquet
+    │   │   └── plof
+    │   │       ├── burden
+    │   │       │   └── eval
+    │   │       │       └── burden_associations.parquet
+    │   │       └── skat
+    │   │           └── eval
+    │   │               └── burden_associations.parquet
+    │   ├── Cholesterol
+    │   │   ├── missense
+    │   │   │   ├── burden
+    │   │   │   │   └── eval
+    │   │   │   │       └── burden_associations.parquet
+    │   │   │   └── skat
+    │   │   │       └── eval
+    │   │   │           └── burden_associations.parquet
+    │   │   └── plof
+    │   │       ├── burden
+    │   │       │   └── eval
+    │   │       │       └── burden_associations.parquet
+    │   │       └── skat
+    │   │           └── eval
+    │   │               └── burden_associations.parquet
+    │   ├── Platelet_count
+    │   │   ├── missense
+    │   │   │   ├── burden
+    │   │   │   │   └── eval
+    │   │   │   │       └── burden_associations.parquet
+    │   │   │   └── skat
+    │   │   │       └── eval
+    │   │   │           └── burden_associations.parquet
+    │   │   └── plof
+    │   │       ├── burden
+    │   │       │   └── eval
+    │   │       │       └── burden_associations.parquet
+    │   │       └── skat
+    │   │           └── eval
+    │   │               └── burden_associations.parquet
+    ├── deeprvat_config.yaml
+    ├── deeprvat.sif
+    ├── gencode.v38.basic.annotation.gtf.gz
+    ├── genotypes.h5
+    ├── phenotypes.parquet
+    ├── protein_coding_genes.parquet
+    └── variants.parquet
+
+[~/my_exp_dir]$ apptainer run deeprvat.sif snakemake -j 1 --snakefile /opt/deeprvat/pipelines/training_association_testing.snakefile --configfile deeprvat_config.yaml --ri -n
diff --git a/containers/apptainer_deeprvat.def b/containers/apptainer_deeprvat.def
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+Bootstrap: docker
+From: mambaorg/micromamba:2.0-ubuntu22.04
+
+%files
+    deeprvat_env.yaml /opt/deeprvat_env.yaml
+%environment
+    export MAMBA_ROOT_PREFIX=/opt/conda
+    export PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
+%post
+    apt-get -y update && apt-get -y install cargo g++
+    micromamba install -q -y -n base -f /opt/deeprvat_env.yaml
+    micromamba clean --all --yes
+
+    micromamba run -n base git clone https://github.com/PMBio/deeprvat /opt/deeprvat
+    micromamba run -n base pip install -e /opt/deeprvat
+%runscript
+    exec micromamba run -n base "$@"
+%labels
+    OWNER: https://github.com/PMBio/deeprvat
+    EnvironmentFile: /opt/deeprvat_env.yaml
+%help
+    This container containes the deepRVAT repository and the relevant
+    Python environment created from an environment file.
+    To run Python from the environment:
+        apptainer run my_environment.sif python
+    To see the environment file used to create the environment:
+        apptainer run my_environment.sif cat /opt/deeprvat_env.yaml
+    To see what packags are in the environment:
+        apptainer run my_environment.sif micromamba list
diff --git a/containers/apptainer_deeprvat_preprocessing.def b/containers/apptainer_deeprvat_preprocessing.def
@@ -0,0 +1,28 @@
+Bootstrap: docker
+From: mambaorg/micromamba:2.0-ubuntu22.04
+
+%files
+    deeprvat_preprocessing_env.yml /opt/deeprvat_preprocessing_env.yml
+%environment
+    export MAMBA_ROOT_PREFIX=/opt/conda
+    export PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
+%post
+    micromamba install -q -y -n base -f /opt/deeprvat_preprocessing_env.yml
+    micromamba clean --all --yes
+
+    micromamba run -n base git clone https://github.com/PMBio/deeprvat /opt/deeprvat
+    micromamba run -n base pip install -e /opt/deeprvat
+%runscript
+    exec micromamba run -n base "$@"
+%labels
+    OWNER: https://github.com/PMBio/deeprvat
+    EnvironmentFile: /opt/deeprvat_preprocessing_env.yml
+%help
+    This container containes the deepRVAT repository and the relevant
+    Python environment created from an environment file.
+    To run Python from the environment:
+        apptainer run my_environment.sif python
+    To see the environment file used to create the environment:
+        apptainer run my_environment.sif cat /opt/deeprvat_preprocessing_env.yml
+    To see what packags are in the environment:
+        apptainer run my_environment.sif micromamba list
diff --git a/containers/deeprvat_env.yaml b/containers/deeprvat_env.yaml
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+name: deeprvat
+channels:
+  - pytorch
+  - nvidia
+  - conda-forge
+  - bioconda
+dependencies:
+  - click=8.1
+  - cudatoolkit=11.8
+  - dask=2023.5
+  - fastparquet=0.5
+  - git
+  - h5py=3.1
+  - mkl==2022.1.0
+  - numcodecs=0.11
+  - numpy=1.21
+  - optuna=2.10
+  - pandas=1.5
+  - pyarrow=11.0
+  - pyranges=0.0.129
+  - python=3.8
+  - pytorch=1.13
+  - pytorch-cuda=11
+  - pytorch-lightning=1.5
+  - pyyaml=5.4
+  - regenie=3.4.1
+  - scikit-learn=1.1
+  - scipy=1.10
+  - setuptools=59.5
+  - snakemake=7.17
+  - sqlalchemy=1.4
+  - statsmodels=0.13
+  - tqdm=4.59
+  - zarr=2.13
+  - Cython=0.29
+  - parallel=20230922
+  - pip=23.0.1
+  - plotnine=0.10.1
+  - pip:
+    - git+https://github.com/HealthML/seak@v0.4.3
+    - bgen==1.6.3
diff --git a/containers/deeprvat_preprocessing_env.yml b/containers/deeprvat_preprocessing_env.yml
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+name: deeprvat_preprocess
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - python=3.8
+  - click=8.1.3
+  - h5py=3.8.0
+  - numpy=1.21.2
+  - pandas=1.5.1
+  - tqdm=4.59.0
+  - pytest=8.2.0
+  - pyarrow=11.0.0
+  - snakemake=7.17.1
+  - bcftools=1.17
+  - htslib=1.19.1
+  - samtools=1.17
+  - mamba=1.4.2
+  - git