Dockerfile

# BSD 3-Clause License
#
# Copyright 2023 The University of Hong Kong, Department of Computer Science
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this
#    list of conditions and the following disclaimer.
#
# 2. Redistributions in binary form must reproduce the above copyright notice,
#    this list of conditions and the following disclaimer in the documentation
#    and/or other materials provided with the distribution.
#
# 3. Neither the name of the copyright holder nor the names of its
#    contributors may be used to endorse or promote products derived from
#    this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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FROM ubuntu:16.04

ENV LANG=C.UTF-8 LC_ALL=C.UTF-8 PATH=/opt/bin:/opt/conda/bin:$PATH

# update ubuntu packages
RUN apt-get update --fix-missing && \
    yes|apt-get upgrade && \
    apt-get install -y \
        wget \
        bzip2 \
        make \
        g++ \
        time \
        libboost-graph-dev && \
    rm -rf /bar/lib/apt/lists/*

WORKDIR /opt/bin

# install anaconda
RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
    bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda && \
    rm Miniconda3-latest-Linux-x86_64.sh && \
    conda config --add channels defaults && \
    conda config --add channels bioconda && \
    conda config --add channels conda-forge && \
    conda create -n clair3_rna -c conda-forge -c bioconda clair3 mosdepth bedtools -y && \
    rm -rf /opt/conda/pkgs/* && \
    rm -rf /root/.cache/pip

ENV PATH /opt/conda/envs/clair3_rna/bin:$PATH
ENV CONDA_DEFAULT_ENV clair3_rna

COPY . .

RUN /bin/bash -c "source activate clair3_rna" && \
    wget http://www.bio8.cs.hku.hk/clair3_rna/models/clair3_rna_models.tar.gz	 -P /opt/models && \
    mkdir -p /opt/conda/envs/clair3_rna/bin/clair3_rna_models && \
    tar -zxvf /opt/models/clair3_rna_models.tar.gz -C /opt/conda/envs/clair3_rna/bin/clair3_rna_models && \
    rm /opt/models/clair3_rna_models.tar.gz && \
    echo 'will cite' | parallel --citation || true \
    echo "source activate clair3_rna" > ~/.bashrc