add docker and data preparing

Dockerfile

@@ -0,0 +1,44 @@
+FROM nvidia/cuda:10.2-cudnn8-runtime-ubuntu18.04
+ENV PATH="/root/miniconda3/bin:${PATH}"
+ARG PATH="/root/miniconda3/bin:${PATH}"
+RUN echo 'Building docker'
+
+COPY ./requirements.txt /opt/app/requirements.txt
+WORKDIR /opt/app
+RUN set -xe \
+    && apt-get update \
+    && apt-get install python3-pip -y
+# RUN pip3 install --upgrade pip
+# RUN python3 -m pip install -i https://pypi.tuna.tsinghua.edu.cn/simple --upgrade pip
+# RUN pip config set global.index-url https://pypi.tuna.tsinghua.edu.cn/simple 
+# RUN pip install -r requirements.txt --default-timeout=1000
+COPY . /opt/app
+
+RUN apt-get update
+RUN apt-get install -y wget && rm -rf /var/lib/apt/lists/*
+RUN wget \
+    https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
+    && mkdir /root/.conda \
+    && bash Miniconda3-latest-Linux-x86_64.sh -b \
+    && rm -f Miniconda3-latest-Linux-x86_64.sh
+RUN conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/ \
+    && conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/ \
+    && conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/
+RUN conda install -c bioconda anarci
+RUN conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch/ \
+    && conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/ \
+    && conda config --set show_channel_urls yes
+RUN conda config --set remote_read_timeout_secs 1000.0
+# RUN conda install -c bioconda anarci
+RUN conda install pytorch==1.10.0 cudatoolkit=10.2 -c pytorch
+
+RUN pip config set global.index-url https://pypi.tuna.tsinghua.edu.cn/simple
+RUN python -m pip install --upgrade pip
+RUN pip install biopython==1.79
+RUN pip install pytorch-lightning==1.6.4
+RUN pip install scikit-learn==1.1.1
+RUN pip install scipy==1.8.1
+RUN pip install tqdm==4.64.0
+RUN pip install pandas==1.4.2
+RUN pip install numpy==1.22.4
+RUN pip install setuptools==59.5.0

README.md

@@ -13,6 +13,10 @@ Both models only takes the primary sequences of CDR3βs and the epitopes as inpu
     ```bash
     conda install -c bioconda anarci
     ```
+We also provided a docker file to facilitate the installation of environment. You can build the docker by runing
+```bash
+docker build -t teim:v1 .
+```
 
 ## Inference
 ### Predict the residue-level interactions of TCR-epitope pairs