mirror of
https://github.com/MillironX/singularity-builds.git
synced 2024-11-24 02:19:55 +00:00
Thomas A. Christensen II
79f1b5735a
Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
125 lines
3.7 KiB
Docker
125 lines
3.7 KiB
Docker
FROM alpine:3.14.3
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LABEL base.image="alpine:3.14.3"
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LABEL software="NanoSim"
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LABEL software.version="3.0.2"
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LABEL dockerfile.version="3"
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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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RUN \
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# Install real dependencies
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apk add --repository http://dl-cdn.alpinelinux.org/alpine/edge/main \
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--update --no-cache \
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bash \
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libbz2 \
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ncurses \
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openblas-dev \
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py3-pip \
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python3 \
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xz \
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zlib && \
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\
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# Install build dependencies
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apk add --repository http://dl-cdn.alpinelinux.org/alpine/edge/main \
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--no-cache --virtual .build-deps \
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blas-dev \
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build-base \
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bzip2-dev \
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freetype-dev \
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g++ \
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gcc \
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gfortran \
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git \
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lapack-dev \
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libgfortran \
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libpng-dev \
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make \
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musl-dev \
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ncurses-dev \
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py-pip \
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python3-dev \
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wget \
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xz-dev \
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zlib-dev &&\
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\
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# Make python3 the default
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ln -fs /usr/include/locale.h /usr/include/xlocale.h && \
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ln -fs /usr/bin/python3 /usr/local/bin/python && \
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ln -fs /usr/bin/pip3 /usr/local/bin/pip && \
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\
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# Download and install Minimap2
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cd /tmp && \
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wget -qO- 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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\
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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 ${LAST_SHA} && \
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make && make install && \
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cd .. && \
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rm -rf last && \
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cd && \
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\
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# Download and install samtools
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cd /tmp && \
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wget https://github.com/samtools/samtools/releases/download/$SAMTOOLS_VERSION/samtools-$SAMTOOLS_VERSION.tar.bz2 && \
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tar xjvf samtools-$SAMTOOLS_VERSION.tar.bz2 && \
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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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\
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# Download and install GenomeTools
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cd /tmp && \
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wget -qO- 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${GENOMETOOLS_VERSION} && \
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cd && \
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\
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# Download and install Python packages
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pip3 install -v --no-cache-dir six==1.16.0 && \
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pip3 install -v --no-cache-dir joblib==0.14.1 && \
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pip3 install -v --no-cache-dir threadpoolctl && \
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pip3 install -v --no-cache-dir numpy==1.17.2 && \
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pip3 install -v --no-cache-dir scipy && \
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pip3 install -v --no-cache-dir cython && \
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pip3 install -v --no-cache-dir scikit-learn==0.21.3 && \
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pip3 install -v --no-cache-dir pysam==0.17 && \
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pip3 install -v --no-cache-dir HTSeq==0.11.2 && \
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pip3 install -v --no-cache-dir pybedtools==0.8.2 && \
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\
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# Download and install NanoSim
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cd /tmp && \
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wget -qO- https://github.com/bcgsc/NanoSim/archive/refs/tags/v${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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\
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# Cleanup build packages
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apk del --no-cache .build-deps
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