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.
62 lines
2.0 KiB
Plaintext
Executable File
62 lines
2.0 KiB
Plaintext
Executable File
ARG CUDA=11.7
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FROM nvidia/cuda:${CUDA}.1-cudnn8-devel-ubuntu22.04
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USER root
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SHELL ["/bin/bash", "-c"]
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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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ARG DEBIAN_FRONTEND=noninteractive
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RUN apt-get update -y && 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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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/*
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# Add the NVIDIA GPG key directly
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RUN wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64/cuda-keyring_1.0-1_all.deb
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RUN dpkg -i cuda-keyring_1.0-1_all.deb && rm cuda-keyring_1.0-1_all.deb
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RUN apt-get -y update && \
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apt-get install -y --no-install-recommends cuda-command-line-tools-11-7
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RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh \
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&& bash miniconda.sh -b -p /opt/conda \
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&& rm miniconda.sh \
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&& ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh \
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&& echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc \
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&& echo "conda activate base" >> ~/.bashrc \
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&& find /opt/conda/ -follow -type f -name '*.a' -delete \
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&& find /opt/conda/ -follow -type f -name '*.js.map' -delete \
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&& /opt/conda/bin/conda clean -afy
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ENV PATH /opt/conda/bin:$PATH
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RUN conda update -y -n base -c defaults conda
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# main conda env (tissue)
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RUN conda create -n tissue python=3.9
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ENV PATH "$PATH:/opt/conda/envs/tissue/bin"
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RUN echo "source activate tissue" >> ~/.bashrc
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RUN conda clean --all -f -y
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# Install packages
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RUN apt-get -y update && apt-get install -y ca-certificates && update-ca-certificates
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RUN /opt/conda/envs/tissue/bin/python3 -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 file
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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 .
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