feat: spec immune dockerfile

SpecImmune/Dockerfile

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+# Use Ubuntu as the base image
+FROM ubuntu:latest
+
+# Install necessary packages and dependencies
+RUN apt-get update && apt-get install -y \
+    wget \
+    software-properties-common \
+    curl \
+    git \
+    unzip \
+    build-essential \
+    && rm -rf /var/lib/apt/lists/*
+
+# Set the working directory
+WORKDIR /SpecImmune
+
+# Define SHELL
+SHELL ["/bin/bash", "-c"] 
+
+RUN git clone https://github.com/deepomicslab/SpecImmune.git /SpecImmune
+RUN cd /SpecImmune; git checkout 96c41fcf7b7b822cc45bd511a7538fc3d879a227
+
+# Download and install Miniconda
+RUN wget -c https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O /tmp/miniconda.sh \
+    && bash /tmp/miniconda.sh -b -p /opt/conda \
+    && rm /tmp/miniconda.sh
+
+# Add Conda to PATH for build steps below
+ENV PATH="/opt/conda/bin:/SpecImmune/bin:${PATH}"
+
+# active conda environment on entry
+COPY docker/entrypoint.sh /opt/conda/bin/entrypoint.sh
+RUN chmod +x /opt/conda/bin/entrypoint.sh
+
+RUN conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/main
+RUN conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/r
+
+# Update Conda
+RUN conda update -n base -c defaults conda -y && \
+    conda clean --all && \
+    conda env create -p /opt/conda/envs/SpecImmune -f /SpecImmune/environment.yml && \
+    conda init
+RUN echo "conda activate SpecImmune" >> ~/.bashrc
+
+# Make SpecImmune the default environment for all exec modes
+# (including Singularity, which ignores ENTRYPOINT and .bashrc).
+# Prepend the env's bin dir to PATH so its python/tools are found first.
+ENV PATH="/opt/conda/envs/SpecImmune/bin:${PATH}" \
+    CONDA_DEFAULT_ENV="SpecImmune" \
+    CONDA_PREFIX="/opt/conda/envs/SpecImmune"
+
+ENTRYPOINT ["/opt/conda/bin/entrypoint.sh"]

SpecImmune/entrypoint.sh

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+#!/bin/bash
+# Enable conda for this shell session
+. /opt/conda/etc/profile.d/conda.sh
+# Activate the specific environment
+conda activate SpecImmune
+# Execute the command passed to the Docker container (e.g., from CMD)
+exec "$@"

SpecImmune/readme.md

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+# SpecImmune Docker Setup and Testing Guide
+
+Place both `Dockerfile` and `.dockerignore` in the same directory.
+
+After completing all make_db operations, move the hg38 files into the `/db` directory. The directory structure should be:
+```
+db/
+├── CYP
+├── hg38/
+│   ├── hg38_no_alt.fa
+│   ├── hg38_no_alt.fa.amb
+│   ├── hg38_no_alt.fa.ann
+│   ├── hg38_no_alt.fa.bwt
+│   ├── hg38_no_alt.fa.fai
+│   ├── hg38_no_alt.fa.pac
+│   └── hg38_no_alt.fa.sa
+├── HLA
+├── HLA_CDS
+├── IG_TR
+├── KIR
+```
+Once the above steps are completed, build the Docker image:
+```
+docker build -t specimmune:v1.0.0 .
+```
+Docker Test Cases
+Display the program help documentation:
+```
+docker run --rm specimmune:v1.0.1
+```
+Define directories:
+```
+dir_db=${specimmune_installed_dir}/db/
+dir_test=${specimmune_installed_dir}/test
+dir_db: The database directory that includes hg38
+dir_test: The test directory containing test data
+```
+Example paths:
+```
+dir_db=/data10/zq123/SpecImmune/db/
+dir_test=/data10/zq123/SpecImmune/test
+```
+Run Test Cases:
+
+Test Case 1: HLA
+```
+docker run --rm -v $dir_db:/SpecImmune/db -v $dir_test:/SpecImmune/test \
+specimmune:v1.0.0 --db /SpecImmune/db -r /SpecImmune/test/HLA/test_HLA_lite.fastq.gz \
+-j 15 -i HLA -n test_HLA -o /SpecImmune/test/test_20250204 \
+--align_method_1 minimap2 -y pacbio
+```
+Test Case 2: KIR
+```
+docker run --rm -v $dir_db:/SpecImmune/db -v $dir_test:/SpecImmune/test \
+specimmune:v1.0.0 --db /SpecImmune/db/ -r /SpecImmune/test/KIR/KIR_dp50_acc98_1.fastq.gz \
+-j 15 -i KIR -n test_new_KIR -o /SpecImmune/test/test_20250204 \
+--hete_p 0.2 --align_method_1 minimap2 -y pacbio
+```
+Test Case 3: IG_TR
+```
+docker run --rm -v $dir_db:/SpecImmune/db -v $dir_test:/SpecImmune/test \
+specimmune:v1.0.0 --db /SpecImmune/db/ -r /SpecImmune/test/IG_TR/vdj.fq.gz \
+-j 15 -i IG_TR -n test_TR -o /SpecImmune/test/test_20250204 -y pacbio \
+--hg38 /SpecImmune/db/hg38/hg38_no_alt.fa --align_method_1 minimap2
+```
+Test Case 4: CYP
+```
+docker run --rm -v $dir_db:/SpecImmune/db -v $dir_test:/SpecImmune/test \
+specimmune:v1.0.0 --db /SpecImmune/db/ -r /SpecImmune/test/CYP/HG03579.CYP.fastq.0.1.fq.gz \
+-j 15 -i CYP -n test_CYP_nano -o /SpecImmune/test/test_20250204 -y nanopore \
+--hg38 /SpecImmune/db/hg38/hg38_no_alt.fa --align_method_1 minimap2
+```
+Run an Interactive Docker Session for Manual Testing
+```
+docker run -it --rm -v $dir_db:/SpecImmune/db -v $dir_test:/SpecImmune/test \
+specimmune:v1.0.0 bash -c "source /opt/conda/bin/activate SpecImmune && \
+python /SpecImmune/scripts/main.py --db /SpecImmune/db/ -r /SpecImmune/test/HLA/test_HLA_lite.fastq.gz \
+-j 15 -i HLA -n test_HLA -o /SpecImmune/test/test_20250204 --align_method_1 minimap2 -y pacbio"
+```
+Now your Docker image is built, and you can run various test cases for SpecImmune!