Digital Trials pipeline configured for WES

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.

Dockerfile_tissue.old

@@ -0,0 +1,61 @@
+ARG CUDA=11.7
+FROM nvidia/cuda:${CUDA}.1-cudnn8-devel-ubuntu22.04
+
+USER root
+SHELL ["/bin/bash", "-c"]
+
+WORKDIR /home
+RUN mkdir -p /home/omic
+WORKDIR /home/omic
+
+ARG DEBIAN_FRONTEND=noninteractive
+RUN apt-get update -y && apt-get install -y --no-install-recommends \
+    build-essential \
+    cmake \
+    curl \
+    git \
+    wget \
+    ca-certificates \
+    hmmer \
+    kalign \
+    tzdata \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+# Add the NVIDIA GPG key directly
+RUN wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64/cuda-keyring_1.0-1_all.deb
+RUN dpkg -i cuda-keyring_1.0-1_all.deb && rm cuda-keyring_1.0-1_all.deb
+RUN apt-get -y update && \
+    apt-get install -y --no-install-recommends cuda-command-line-tools-11-7
+
+RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh \
+    && bash miniconda.sh -b -p /opt/conda \
+    && rm miniconda.sh \
+    && ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh \
+    && echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc \
+    && echo "conda activate base" >> ~/.bashrc \
+    && find /opt/conda/ -follow -type f -name '*.a' -delete \
+    && find /opt/conda/ -follow -type f -name '*.js.map' -delete \
+    && /opt/conda/bin/conda clean -afy
+
+ENV PATH /opt/conda/bin:$PATH
+RUN conda update -y -n base -c defaults conda
+
+# main conda env (tissue)
+RUN conda create -n tissue python=3.9
+ENV PATH "$PATH:/opt/conda/envs/tissue/bin"
+RUN echo "source activate tissue" >> ~/.bashrc
+RUN conda clean --all -f -y
+
+# Install packages
+RUN apt-get -y update && apt-get install -y ca-certificates && update-ca-certificates
+RUN /opt/conda/envs/tissue/bin/python3 -m pip install pandas numpy
+
+# Package into python script for running in nextflow
+COPY drug_tissue_distribution.py /home/omic/drug_tissue_distribution.py
+RUN chmod +x /home/omic/drug_tissue_distribution.py
+
+# copy reference file
+COPY HPA_normal_ihc_data.tsv .
+COPY MANE_all_transcipts.csv .
+COPY digital_patient_extract_metrics.py .