Commit 9985aec3 authored by Damien VINTACHE's avatar Damien VINTACHE

add Dockerfile to run the pipeline with docker and conda

parent 77b83ec4
FROM ubuntu:18.04
RUN ln -fs /usr/share/zoneinfo/Europe/Paris /etc/localtime
RUN apt-get update
RUN apt-get install -yy git curl
# RUN pip3 install -qq snakemake jsonschema gitpython pandas
RUN curl -LO https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
RUN bash Miniconda3-latest-Linux-x86_64.sh -p /miniconda -b
RUN rm Miniconda3-latest-Linux-x86_64.sh
ENV PATH=/miniconda/bin:${PATH}
# RUN conda update -n base -c defaults conda
RUN conda config --add channels conda-forge
RUN conda config --add channels bioconda
RUN conda create -n microsysmics snakemake pandas jsonschema gitpython
# RUN mkdir -p /home/microSysMics
COPY . /home/microSysMics
# build and install
WORKDIR /home/microSysMics/
# RUN for file in conda/*.yml; do conda env create --file $file; done;
# RUN conda env create --file conda/fastqc.yml
# RUN conda env create --file conda/microSysMics.yml
# RUN conda env create --file conda/multiqc.yml
# RUN conda env create --file conda/qiime2-2019.4-py36-linux-conda.yml
# run snakemake in dry run mode
# RUN /bin/bash -c 'conda init bash && . activate microsysmics && snakemake -p --use-conda --snakefile Snakefile.dummy'
CMD /bin/bash -c 'conda init bash && . activate microsysmics && snakemake -p --use-conda'
# docker build -t microsysmics -f Dockerfile.microSysMics .
# docker run -e LC_ALL=C.UTF-8 -e LANG=C.UTF-8 -e TZ=Europe/Paris -t microsysmics
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