Dockerfile

FROM conda/miniconda3

LABEL Name=hicstuff Version=3.2.3

RUN echo "deb http://archive.debian.org/debian stretch main contrib non-free" > /etc/apt/sources.list

RUN apt-get update && apt-get install -y procps bash git

RUN conda update -y -n base -c defaults conda \
&& git clone https://github.com/koszullab/hicstuff.git \
&& cd hicstuff \
&& git checkout v3.2.3 \
&& conda init \
&& conda config --add channels r \
&& conda config --add channels defaults \
&& conda config --add channels conda-forge \
&& conda config --add channels bioconda \
&& conda create -y -n hicstuff
SHELL ["conda", "run", "-n", "hicstuff", "/bin/bash", "-c"]
RUN conda install -c conda-forge -y \
    pairtools \
    pip \
    bowtie2 \
    minimap2 \
    bwa \
    samtools \
    htslib \
    cooler \
&& conda clean -afy \
&& cd hicstuff \
&& sed -i 's/pairtools//g' requirements.txt \
&& pip install -Ur requirements.txt \
&& pip install pysam cython \
&& pip install . \
#&& pip install pairtools \
&& chmod -R +x /usr/local/lib/python3.10/ \
&& chmod -R +x /usr/local/lib/python3.10/lib-dynload/ \
&& echo "conda activate hicstuff" >> /root/.bashrc
ENV PATH /usr/local/envs/hicstuff/bin:/usr/local/condabin:$PATH