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Dockerfile
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FROM python:3.12-slim@sha256:2be8daddbb82756f7d1f2c7ece706aadcb284bf6ab6d769ea695cc3ed6016743
LABEL authors="phil.ewels@seqera.io,erik.danielsson@scilifelab.se" \
description="Docker image containing requirements for nf-core/tools"
# Do not pick up python packages from $HOME
ENV PYTHONNUSERSITE=1
# Update pip to latest version
RUN python -m pip install --upgrade pip
# Install dependencies
COPY requirements.txt requirements.txt
RUN python -m pip install -r requirements.txt
# Install Nextflow dependencies
RUN apt-get update \
&& apt-get upgrade -y \
&& apt-get install -y git \
&& apt-get install -y curl
# Create man dir required for Java installation
# and install Java
RUN mkdir -p /usr/share/man/man1 \
&& apt-get install -y default-jre \
&& apt-get clean -y && rm -rf /var/lib/apt/lists/*
# Setup ARG for NXF_VER ENV
ARG NXF_VER=""
ENV NXF_VER ${NXF_VER}
# Install Nextflow
RUN curl -s https://get.nextflow.io | bash \
&& mv nextflow /usr/local/bin \
&& chmod a+rx /usr/local/bin/nextflow
# Install nf-test
RUN curl -fsSL https://code.askimed.com/install/nf-test | bash \
&& mv nf-test /usr/local/bin \
&& chmod a+rx /usr/local/bin/nf-test
# Add the nf-core source files to the image
COPY . /usr/src/nf_core
WORKDIR /usr/src/nf_core
# Install nf-core
RUN python -m pip install .
# Set up entrypoint and cmd for easy docker usage
ENTRYPOINT [ "nf-core" ]
CMD [ "." ]