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.old2

@@ -0,0 +1,56 @@
+# Use the specified Micromamba base image with CUDA 11.7
+FROM mambaorg/micromamba:2.1.1-cuda11.7.1-ubuntu20.04
+
+
+USER root
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+
+# WORKDIR /home
+# RUN mkdir -p /home/omic
+WORKDIR /home/omic
+
+# Install system packages
+ARG DEBIAN_FRONTEND=noninteractive
+RUN micromamba install -y python=3.9 pandas numpy && \
+    pip install pandas numpy && \
+    micromamba clean --all --yes
+
+# Add the NVIDIA GPG key directly
+RUN apt-get -y update \
+    && apt-get install -y --no-install-recommends \
+        build-essential \
+        cmake \
+        curl \
+        git \
+        wget \
+        ca-certificates \
+        hmmer \
+        kalign \
+        tzdata \
+    && wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64/cuda-keyring_1.0-1_all.deb \
+    && dpkg -i cuda-keyring_1.0-1_all.deb && rm cuda-keyring_1.0-1_all.deb \
+    && apt-get install -y --no-install-recommends cuda-command-line-tools-11-7 \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+
+# Switch to the mamba user for micromamba operations
+# USER $MAMBA_USER
+# WORKDIR /home/omic
+
+# Install Python and packages into the base environment
+
+# Activate the base environment for subsequent RUN commands
+# ARG MAMBA_DOCKERFILE_ACTIVATE=1
+
+# # Install Python packages with pip (now runs in the activated environment)
+# RUN python -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 files
+COPY HPA_normal_ihc_data.tsv .
+COPY MANE_all_transcipts.csv .
+COPY digital_patient_extract_metrics.py .