.gitpod.Dockerfile

FROM gitpod/workspace-full:2023-03-24-02-48-18

ENV RETRIGGER=4

ENV BUILDKIT_VERSION=0.11.6
ENV BUILDKIT_FILENAME=buildkit-v${BUILDKIT_VERSION}.linux-amd64.tar.gz
ENV DAZZLE_VERSION=0.1.17

USER root

# Install dazzle, buildkit and pre-commit
RUN curl -sSL https://github.com/moby/buildkit/releases/download/v${BUILDKIT_VERSION}/${BUILDKIT_FILENAME} | tar -xvz -C /usr
RUN curl -sSL https://github.com/gitpod-io/dazzle/releases/download/v${DAZZLE_VERSION}/dazzle_${DAZZLE_VERSION}_Linux_x86_64.tar.gz | tar -xvz -C /usr/local/bin
RUN curl -sSL https://github.com/mvdan/sh/releases/download/v3.5.1/shfmt_v3.5.1_linux_amd64 -o /usr/bin/shfmt \
    && chmod +x /usr/bin/shfmt
RUN install-packages shellcheck \
    && pip3 install pre-commit
RUN curl -sSL https://github.com/mikefarah/yq/releases/download/v4.22.1/yq_linux_amd64 -o /usr/bin/yq && chmod +x /usr/bin/yq

# Apptainer installation
RUN apt-get update && \
    apt-get install -y software-properties-common && \
    add-apt-repository -y ppa:apptainer/ppa && \
    apt-get update && \
    apt-get install -y apptainer

# Mambaforge installation
RUN wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh && \
    sh Mambaforge-Linux-x86_64.sh -b -p /home/gitpod/mambaforge && \
    /home/gitpod/mambaforge/bin/mamba create -n snakemake -c bioconda -c conda-forge snakemake && \
    /home/gitpod/mambaforge/bin/mamba init && \
    echo "source /home/gitpod/mambaforge/bin/activate" >> /home/gitpod/.bashrc && \
    echo "conda activate snakemake" >> /home/gitpod/.bashrc

# Clean up to reduce image size
RUN apt-get clean && \
    rm -rf /var/lib/apt/lists/* && \
    rm Mambaforge-Linux-x86_64.sh