mirror of
https://github.com/MillironX/singularity-builds.git
synced 2024-11-23 18:09:55 +00:00
Thomas A. Christensen II
12a8ac3490
Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
119 lines
3.4 KiB
Docker
119 lines
3.4 KiB
Docker
FROM ubuntu:focal
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LABEL base.image="ubuntu:focal"
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LABEL software="NanoSim"
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LABEL software.version="3.0.2"
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LABEL dockerfile.version="4"
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LABEL description="Fast and scalable read simulator that captures the technology-specific features of ONT data."
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LABEL website="https://github.com/bcgsc/NanoSim"
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LABEL license="https://github.com/bcgsc/NanoSim/blob/master/LICENSE"
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LABEL maintainer="Thomas A. Christensen II"
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LABEL maintainer.email="25492070+MillironX@users.noreply.github.com"
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ARG NANOSIM_VERSION=3.0.2
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ARG MINIMAP2_VERSION=2.18
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ARG LAST_VERSION=916
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ARG LAST_SHA="98fc3d382ef443b4468b633d2fe90ac3d0b3c21e"
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ARG SAMTOOLS_VERSION=1.12
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ARG GENOMETOOLS_VERSION=1.6.2
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ENV DEBIAN_FRONTEND noninteractive
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ENV DEBCONF_NONINTERACTIVE_SEEN true
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RUN \
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# Install real dependencies
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apt-get update && \
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apt-get install --no-install-recommends -y \
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build-essential \
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bzip2 \
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ca-certificates \
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curl \
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cython3 \
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gcc \
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git \
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gnuplot \
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libbz2-dev \
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libcurl4-gnutls-dev \
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liblzma-dev \
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libncurses5-dev \
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libssl-dev \
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make \
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perl \
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python3 \
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python3-pip \
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python3-dev \
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zlib1g-dev \
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&& \
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apt-get autoclean && rm -rf /var/lib/apt/lists/*
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RUN \
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# Make python3 the default
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update-alternatives --install /usr/bin/python python /usr/bin/python3 1 && \
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update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 1
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RUN \
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# Download and install Minimap2
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cd /tmp && \
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curl -L https://github.com/lh3/minimap2/releases/download/v${MINIMAP2_VERSION}/minimap2-${MINIMAP2_VERSION}.tar.bz2 | tar xjv && \
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cd minimap2-${MINIMAP2_VERSION} && \
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make && \
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cp minimap2 /usr/bin && \
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mkdir /usr/man && \
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cp minimap2.1 /usr/man && \
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cd .. && \
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rm -rf minimap2-${MINIMAP2_VERSION} && \
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cd
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RUN \
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# Download and install LAST
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cd /tmp && \
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git clone https://gitlab.com/mcfrith/last.git && \
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cd last && \
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git checkout ${LAST_SHA} && \
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make && make install && \
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cd .. && \
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rm -rf last && \
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cd
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RUN \
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# Download and install samtools
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cd /tmp && \
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curl -L https://github.com/samtools/samtools/releases/download/$SAMTOOLS_VERSION/samtools-$SAMTOOLS_VERSION.tar.bz2 | tar xvj && \
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cd samtools-$SAMTOOLS_VERSION && \
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./configure && \
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make && make install && \
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cd .. && \
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rm -rf samtools-$SAMTOOLS_VERSION && \
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cd
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RUN \
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# Download and install GenomeTools
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cd /tmp && \
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curl -L https://github.com/genometools/genometools/archive/refs/tags/v${GENOMETOOLS_VERSION}.tar.gz | tar xzv && \
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cd genometools-${GENOMETOOLS_VERSION} && \
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make cairo=no errorcheck=no && make cairo=no errorcheck=no install && \
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cd .. && \
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rm -rf v${GENOMETOOLS_VERSION} && \
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cd
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# Download and install Python packages from pip
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RUN pip3 install -v --no-cache-dir six==1.16.0
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RUN pip3 install -v --no-cache-dir joblib==0.14.1
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RUN pip3 install -v --no-cache-dir numpy==1.17.2
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RUN pip3 install -v --no-cache-dir scipy==1.4.1
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RUN pip3 install -v --no-cache-dir scikit-learn==0.21.3
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RUN pip3 install -v --no-cache-dir pysam==0.17
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RUN pip3 install -v --no-cache-dir HTSeq==0.11.2
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RUN pip3 install -v --no-cache-dir pybedtools==0.8.2
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RUN \
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# Download and install NanoSim
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cd /tmp && \
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curl -L https://github.com/bcgsc/NanoSim/archive/refs/tags/v${NANOSIM_VERSION}.tar.gz | tar xzv && \
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cd NanoSim-${NANOSIM_VERSION} && \
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cp -r src/* /usr/bin && \
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cd .. && \
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rm -rf NanoSim-${NANOSIM_VERSION} && \
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cd ..
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ENTRYPOINT [ "/usr/bin/simulator.py" ]
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