Dockerfile

# bsub -G compute-oncology -q oncology-interactive -Is -a 'docker_build(griffithlab/neoang_scripts)' -- --tag griffithlab/neoang_scripts .

FROM python:3.8-slim-buster

RUN ["apt-get", "update"]
RUN ["apt-get", "install", "-y", "vim"]

ADD scripts/get_FDA_thresholds.py /opt/scripts/get_FDA_thresholds.py
ADD scripts/get_neoantigen_qc.py /opt/scripts/get_neoantigen_qc.py
ADD scripts/requirements.txt /opt/scripts/requirements.txt
ADD scripts/fda_quality_thresholds.csv /opt/scripts/fda_quality_thresholds.csv
ADD scripts/generate_reviews_files.py /opt/scripts/generate_reviews_files.py
ADD scripts/bold_classII.py /opt/scripts/bold_classII.py
ADD scripts/color_peptides51mer.py /opt/scripts/color_peptides51mer.py
ADD scripts/setup_review.py /opt/scripts/setup_review.py
ADD scripts/modify_peptides.py /opt/scripts/modify_peptides.py
ADD scripts/hla_comparison.py /opt/scripts/hla_comparison.py

RUN chmod +r /opt/scripts/*


RUN pip install --upgrade pip


RUN pip3 install -r /opt/scripts/requirements.txt