PRIME1.0 도커 파일

# PRIME1.0 and MixMHCpred-2.0.2
FROM ubuntu:18.04

#COPY . mhcnuggets
ENV TZ=Asia/Seoul
ARG DEBIAN_FRONTEND=noninteractive # 이걸 해야 선택옵션 없어짐


#FROM ubuntu:18.04
RUN apt-get update
RUN apt-get -y install software-properties-common
RUN add-apt-repository ppa:deadsnakes/ppa

# 파이썬 설치
#RUN apt-get -y install python3.5
#RUN update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.5 1

RUN mkdir /workdir
WORKDIR /workdir
RUN apt-get update && apt upgrade -y
RUN apt install -y software-properties-common vim 
RUN add-apt-repository ppa:deadsnakes/ppa -y
#RUN apt install software-properties-common wget -y
#RUN cd /workdir
#RUN wget https://www.python.org/ftp/python/3.11.1/Python-3.11.1.tar.xz
#RUN tar -xf Python-3.11.1.tar.xz
#RUN cd Python-3.11.1
#RUN ./configure --enable-optimizations
#RUN make altinstall
RUN apt-get install python3.10 -y # --no-install-recommends
#RUN echo $(apt list | grep python3)
#RUN echo $(which python3)
#RUN echo $(ls /usr/bin/ | grep python)
#RUN echo $(python3 -V)
#RUN update-alternatives --install /usr/local/bin/python3 python3 /usr/bin/python3.10 1
#RUN update-alternatives --install /usr/bin/python python /usr/bin/python3.10 1

# 파이썬 라이브러리 설치
RUN apt-get -y install python3-pip
RUN apt-get install -y curl wget unzip vim less
#RUN curl -sS https://bootstrap.pypa.io/get-pip.py #| python3.10
#RUN python3.10 -m pip --version
#RUN pip3 install --upgrade --ignore-installed pip setuptools

# MixMHCpred 설치
RUN mkdir /tools
WORKDIR /tools
RUN mkdir MixMHCpred
WORKDIR /tools/MixMHCpred
RUN wget https://github.com/GfellerLab/MixMHCpred/archive/refs/tags/v2.0.2.zip
RUN unzip v2.0.2.zip
WORKDIR /tools/MixMHCpred/MixMHCpred-2.0.2
RUN echo $(pwd)
RUN cp MixMHCpred MixMHCpred-original
RUN sed -i 's/lib_path="YOUR PATH TO MixMHCpred\/lib FOLDER"/lib_path="\/tools\/MixMHCpred\/MixMHCpred-2.0.2\/lib"/' MixMHCpred
WORKDIR /tools/MixMHCpred/MixMHCpred-2.0.2/lib
RUN g++ -O3 MixMHCpred.cc -o MixMHCpred.x
WORKDIR /tools/MixMHCpred/MixMHCpred-2.0.2/
RUN ./MixMHCpred -i test/test.fa -o test/out.txt -a A0101,A2501,B0801,B1801 # 테스트 용도

# PRIME 설치
RUN mkdir -p /tools/PRIME/PRIME1.0 
WORKDIR /tools/PRIME/PRIME1.0
RUN wget https://github.com/GfellerLab/PRIME/archive/refs/tags/v1.0.zip
RUN unzip v1.0.zip
WORKDIR /tools/PRIME/PRIME1.0/PRIME-1.0
RUN cp PRIME PRIME-original
RUN sed -i 's/lib_path="\/app\/PRIME\/lib"/lib_path="\/tools\/PRIME\/PRIME1.0\/PRIME-1.0\/lib"/' PRIME
RUN sed -i '102i MixMHCpred="/tools/MixMHCpred/MixMHCpred-2.0.2/MixMHCpred"' PRIME
RUN ./PRIME -i test/test.txt -o test/out.txt -a A0201,A0101