9e75f44f1a
Source-only snapshot of the cluster branch for WES execution. Large reference files (HPA/MANE/ensemble FASTA, model weights, ~597 MB) are omitted: they are baked into the container images at build time and mounted from the dreamdock-data PVC at runtime, and exceed the Gitea request size limit. Pipeline entry point is main.nf, which orchestrates the biotransformer, conplex and tissue modules as a single workflow. Ligand inputs are read from the eureka workspace; protein_zarr and chembl_db come from the dreamdock-data PVC.
56 lines
1.6 KiB
Plaintext
Executable File
56 lines
1.6 KiB
Plaintext
Executable File
# Use the specified Micromamba base image with CUDA 11.7
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FROM mambaorg/micromamba:2.1.1-cuda11.7.1-ubuntu20.04
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USER root
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ARG MAMBA_DOCKERFILE_ACTIVATE=1
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# WORKDIR /home
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# RUN mkdir -p /home/omic
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WORKDIR /home/omic
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# Install system packages
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ARG DEBIAN_FRONTEND=noninteractive
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RUN micromamba install -y python=3.9 pandas numpy && \
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pip install pandas numpy && \
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micromamba clean --all --yes
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# Add the NVIDIA GPG key directly
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RUN apt-get -y update \
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&& apt-get install -y --no-install-recommends \
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build-essential \
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cmake \
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curl \
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git \
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wget \
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ca-certificates \
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hmmer \
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kalign \
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tzdata \
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&& wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64/cuda-keyring_1.0-1_all.deb \
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&& dpkg -i cuda-keyring_1.0-1_all.deb && rm cuda-keyring_1.0-1_all.deb \
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&& apt-get install -y --no-install-recommends cuda-command-line-tools-11-7 \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/*
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# Switch to the mamba user for micromamba operations
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# USER $MAMBA_USER
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# WORKDIR /home/omic
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# Install Python and packages into the base environment
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# Activate the base environment for subsequent RUN commands
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# ARG MAMBA_DOCKERFILE_ACTIVATE=1
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# # Install Python packages with pip (now runs in the activated environment)
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# RUN python -m pip install pandas numpy
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# Package into python script for running in nextflow
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COPY drug_tissue_distribution.py /home/omic/drug_tissue_distribution.py
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RUN chmod +x /home/omic/drug_tissue_distribution.py
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# Copy reference files
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COPY HPA_normal_ihc_data.tsv .
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COPY MANE_all_transcipts.csv .
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COPY digital_patient_extract_metrics.py . |