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Dockerfile
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Dockerfile
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# Use the official micromamba image as a base
FROM mambaorg/micromamba:latest
# Set the base layer for micromamba
USER root
# Update package manager and install essential build tools
RUN apt-get update && apt-get install -y \
build-essential \
git \
procps \
wget \
apt-transport-https \
ca-certificates \
curl \
gnupg-agent \
software-properties-common
# Use Docker's convenience script to install the latest Docker
RUN curl -fsSL https://get.docker.com -o get-docker.sh && sh get-docker.sh
ARG MAMBA_ROOT_PREFIX=/opt/conda
# Add /opt/conda/bin to the PATH
ENV PATH $MAMBA_ROOT_PREFIX/bin:$PATH
# Install bioconda-utils and grayskull using micromamba
RUN micromamba install -y -c conda-forge -c bioconda \
bioconda-utils \
pip \
--prefix $MAMBA_ROOT_PREFIX \
&& micromamba clean --all --yes
# Install grayskull using pip
RUN pip install grayskull
# Cleanup the Docker installation script
RUN rm get-docker.sh
# Note on Docker daemon access:
# To use Docker inside the container, you need to run the container with the Docker daemon socket mounted.
# This is typically done with the following Docker run option:
# -v /var/run/docker.sock:/var/run/docker.sock