rliterman@0: # CSP2 Dockerfile
rliterman@0: # Based on StaPH-B's Dockerfile for BEDTools, MUmmer, and Skesa
rliterman@0: # Thanks to Erin Young, Curtis Kapsak, John Arnn, and the StaPH-B team
rliterman@0: # https://github.com/StaPH-B/docker-builds/blob/master/bedtools/2.31.1/Dockerfile
rliterman@0: # https://github.com/StaPH-B/docker-builds/blob/master/mummer/4.0.0/Dockerfile
rliterman@0: # https://github.com/StaPH-B/docker-builds/blob/master/skesa/2.4.0/Dockerfile
rliterman@0: 
rliterman@0: ARG CSP2_VER="0.9.0"
rliterman@0: ARG BEDTOOLS_VER="2.31.1"
rliterman@0: ARG MUMMER_VER="4.0.0"
rliterman@0: ARG SKESA_VER="2.4.0"
rliterman@0: ARG MASH_VER="2.3"
rliterman@0: ARG BBMAP_VER="38.90"
rliterman@0: ARG PYTHON_VER="3.8"
rliterman@0: 
rliterman@0: FROM ubuntu:focal AS build
rliterman@0: 
rliterman@0: ARG BEDTOOLS_VER
rliterman@0: ARG MUMMER_VER
rliterman@0: ARG SKESA_VER
rliterman@0: ARG MASH_VER
rliterman@0: ARG BBMAP_VER
rliterman@0: ARG PYTHON_VER
rliterman@0: 
rliterman@0: WORKDIR /build
rliterman@0: 
rliterman@0: # to prevent tzdata from asking for a region during apt updates; ARG so that variable only 
rliterman@0: # persists at buildtime
rliterman@0: # from https://github.com/StaPH-B/docker-builds/blob/master/mummer/4.0.0/Dockerfile
rliterman@0: ARG DEBIAN_FRONTEND=noninteractive
rliterman@0: 
rliterman@0: # Install build dependencies
rliterman@0: RUN apt-get update && apt-get install -y --no-install-recommends \
rliterman@0:     tzdata \
rliterman@0:     gpg-agent \
rliterman@0:     software-properties-common \
rliterman@0:     build-essential \
rliterman@0:     zlib1g-dev \
rliterman@0:     libghc-bzlib-dev \
rliterman@0:     liblzma-dev \
rliterman@0:     wget \
rliterman@0:     ca-certificates 
rliterman@0: 
rliterman@0: RUN add-apt-repository 'ppa:deadsnakes/ppa' && apt-get update && apt-get install -y --no-install-recommends \
rliterman@0:     python${PYTHON_VER} \
rliterman@0: #    python${PYTHON_VER}-pip \
rliterman@0: #    python${PYTHON_VER}-full \
rliterman@0:     python${PYTHON_VER}-dev \
rliterman@0:     python${PYTHON_VER}-venv && \
rliterman@0:     python${PYTHON_VER} -m venv --copies /opt/venv
rliterman@0: 
rliterman@0: 
rliterman@0: ENV PATH="/opt/venv/bin:$PATH"
rliterman@0: 
rliterman@0: RUN pip install --no-cache-dir -U pandas~=1.2.0 pybedtools refchooser scikit-learn
rliterman@0: 
rliterman@0: ADD https://github.com/arq5x/bedtools2/archive/refs/tags/v${BEDTOOLS_VER}.tar.gz .
rliterman@0: ADD https://github.com/mummer4/mummer/releases/download/v${MUMMER_VER}rc1/mummer-${MUMMER_VER}rc1.tar.gz .
rliterman@0: ADD https://github.com/ncbi/SKESA/releases/download/${SKESA_VER}/skesa.centos.7.7 .
rliterman@0: ADD https://github.com/ncbi/SKESA/releases/download/${SKESA_VER}/gfa_connector.centos7.7 .
rliterman@0: ADD https://github.com/ncbi/SKESA/releases/download/${SKESA_VER}/kmercounter.centos7.7 .
rliterman@0: ADD https://github.com/marbl/Mash/releases/download/v${MASH_VER}/mash-Linux64-v${MASH_VER}.tar .
rliterman@0: 
rliterman@0: # Install BEDTools
rliterman@0: # per https://github.com/StaPH-B/docker-builds/blob/master/bedtools/2.31.1/Dockerfile
rliterman@0: # python3 required when compiling via `make` command for creating old CLI executables
rliterman@0: # dependencies listed here (albeit for v2.30.0, still should be identical): https://packages.ubuntu.com/jammy/bedtools
rliterman@0: # requires libghc-bzlib-dev, build-essential, zlib1g-dev, and a few others
rliterman@0: # 'make install' should place binary executable files in /usr/local/bin
rliterman@0: RUN tar -xzf v${BEDTOOLS_VER}.tar.gz && \
rliterman@0:     rm v${BEDTOOLS_VER}.tar.gz && \
rliterman@0:    cd bedtools2-${BEDTOOLS_VER} && \
rliterman@0:    make && \
rliterman@0:    make install 
rliterman@0: 
rliterman@0:  # Install mummer
rliterman@0:  # per https://github.com/StaPH-B/docker-builds/blob/master/mummer/4.0.0/Dockerfile
rliterman@0: RUN tar -xvf mummer-${MUMMER_VER}rc1.tar.gz && \
rliterman@0:     rm mummer-${MUMMER_VER}rc1.tar.gz && \
rliterman@0:     cd mummer-${MUMMER_VER}rc1 && \
rliterman@0:     ./configure --prefix=/usr/local && \
rliterman@0:     make && \
rliterman@0:     make install && \
rliterman@0:     ldconfig
rliterman@0: 
rliterman@0: # # Install Skesa
rliterman@0: # # per https://github.com/StaPH-B/docker-builds/blob/master/skesa/2.4.0/Dockerfile
rliterman@0: # # get skesa, gfa_connector, and kmercounter binaries, rename them
rliterman@0: RUN mkdir skesa && \
rliterman@0:     cd skesa && \
rliterman@0:     mv /build/skesa.centos.7.7 skesa && \
rliterman@0:     mv /build/gfa_connector.centos7.7 gfa_connector && \
rliterman@0:     mv /build/kmercounter.centos7.7 kmercounter && \
rliterman@0:     chmod +x skesa gfa_connector kmercounter && \
rliterman@0:     mv skesa gfa_connector kmercounter /usr/local/bin
rliterman@0: 
rliterman@0: # Install Mash
rliterman@0: RUN tar -xvf mash-Linux64-v${MASH_VER}.tar && \
rliterman@0:     mv mash-Linux64-v${MASH_VER}/mash /usr/local/bin
rliterman@0: 
rliterman@0: # Install BBMap
rliterman@0: RUN wget -O BBMap_${BBMAP_VER}.tar.gz https://sourceforge.net/projects/bbmap/files/BBMap_${BBMAP_VER}.tar.gz/download && \
rliterman@0:     tar -xvf BBMap_${BBMAP_VER}.tar.gz && \
rliterman@0:     mv bbmap/* /usr/local/bin
rliterman@0: 
rliterman@0: 
rliterman@0: FROM ubuntu:focal AS app
rliterman@0: 
rliterman@0: ARG CSP2_VER
rliterman@0: ARG CSP2_BRANCH="main"
rliterman@0: ARG PYTHON_VER
rliterman@0: 
rliterman@0: LABEL base.image="ubuntu:focal"
rliterman@0: LABEL version=${CSP2_VER}
rliterman@0: LABEL software="CSP2"
rliterman@0: LABEL software.version=${CSP2_VER}
rliterman@0: LABEL description="a Nextflow pipeline for rapid, accurate SNP distance estimation from assembly data"
rliterman@0: LABEL website="https://github.com/CFSAN-Biostatistics/CSP2"
rliterman@0: LABEL licence="https://github.com/CFSAN-Biostatistics/CSP2/blob/main/LICENSE"
rliterman@0: LABEL maintainer="Robert Literman"
rliterman@0: LABEL maintainer.email="Robert.Literman@fda.hhs.gov"
rliterman@0: LABEL maintainer.organization="FDA/CFSAN/Biostatistics"
rliterman@0: LABEL maintainer2="Justin Payne"
rliterman@0: LABEL maintainer2.email="Justin.Payne@fda.hhs.gov"
rliterman@0: LABEL maintainer2.organization="FDA/CFSAN/Biostatistics"
rliterman@0: 
rliterman@0: WORKDIR /root/.nextflow
rliterman@0: WORKDIR /app
rliterman@0: 
rliterman@0: # copy in all executable files from builder stage to final app stage
rliterman@0: COPY --from=build /usr/local/bin /usr/local/bin
rliterman@0: 
rliterman@0: # Lots of perl nonsense
rliterman@0: COPY --from=build /usr/local/lib /usr/local/lib
rliterman@0: COPY --from=build /usr/local/libexec/mummer /usr/local/libexec/mummer
rliterman@0: COPY --from=build /usr/lib/x86_64-linux-gnu/perl /usr/lib/x86_64-linux-gnu/perl
rliterman@0: COPY --from=build /usr/local/share /usr/local/share
rliterman@0: COPY --from=build /usr/share /usr/share
rliterman@0: COPY --from=build /opt/venv /opt/venv
rliterman@0: COPY --from=build /usr/bin/make /usr/local/bin/make
rliterman@0: 
rliterman@0: 
rliterman@0: # Python stuff
rliterman@0: COPY --from=build /usr/lib/python${PYTHON_VER} /usr/lib/python${PYTHON_VER}
rliterman@0: 
rliterman@0: 
rliterman@0: #Install JRE
rliterman@0: RUN apt-get update && apt-get install -y --no-install-recommends \
rliterman@0:     ca-certificates \
rliterman@0:     openjdk-17-jre-headless \
rliterman@0:     curl
rliterman@0: 
rliterman@0: # Install Nextflow
rliterman@0: # per https://www.nextflow.io/docs/latest/getstarted.html
rliterman@0: RUN export CAPSULE_LOG=debug && curl -s https://get.nextflow.io | bash && \
rliterman@0:     chmod +x nextflow && \
rliterman@0:     mv nextflow /usr/local/bin && \
rliterman@0:     nextflow run hello
rliterman@0: 
rliterman@0: ADD docker/Makefile .
rliterman@0: 
rliterman@0: # set PATH, set perl locale settings for singularity compatibility
rliterman@0: ENV PATH="/opt/venv/bin:/usr/local/bin:/skesa:$PATH" \
rliterman@0:     LC_ALL=C \
rliterman@0:     NXF_OFFLINE='true'
rliterman@0: 
rliterman@0: ADD bin ./bin
rliterman@0: ADD conf ./conf
rliterman@0: ADD subworkflows ./subworkflows
rliterman@0: ADD CSP2.nf ./CSP2.nf
rliterman@0: ADD nextflow.config ./nextflow.config
rliterman@0: 
rliterman@0: 
rliterman@0: FROM app AS pretest
rliterman@0: 
rliterman@0: # set PATH, set perl locale settings for singularity compatibility
rliterman@0: ENV PATH="/opt/venv/bin:/usr/local/bin:/skesa:$PATH" \
rliterman@0:     LC_ALL=C \
rliterman@0:     NXF_OFFLINE='true'
rliterman@0: 
rliterman@0: #Alternate test data directory
rliterman@0: ADD https://github.com/CFSAN-Biostatistics/CSP2_TestData#main:assets assets/
rliterman@0: 
rliterman@0: 
rliterman@0: # Test MUmmer installation
rliterman@0: # per https://github.com/StaPH-B/docker-builds/blob/master/mummer/4.0.0/Dockerfile
rliterman@0: 
rliterman@0: ADD https://mummer4.github.io/tutorial/exampleFiles/2.1/in/H_pylori26695_Eslice.fasta .
rliterman@0: ADD https://mummer4.github.io/tutorial/exampleFiles/2.1/in/H_pyloriJ99_Eslice.fasta .
rliterman@0: ADD https://mummer4.github.io/tutorial/exampleFiles/2.2/in/B_anthracis_Mslice.fasta .
rliterman@0: ADD https://mummer4.github.io/tutorial/exampleFiles/2.2/in/B_anthracis_contigs.fasta .
rliterman@0: ADD http://mummer.sourceforge.net/examples/data/H_pylori26695_Eslice.fasta .
rliterman@0: ADD http://mummer.sourceforge.net/examples/data/H_pyloriJ99_Eslice.fasta .
rliterman@0: ADD https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V5.3.2/SARS-CoV-2.primer.bed ./V5.3.2.artic.bed
rliterman@0: ADD https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V4.1/SARS-CoV-2.primer.bed ./V4.1.artic.bed
rliterman@0: 
rliterman@0: FROM pretest AS test
rliterman@0: 
rliterman@0: # Test MASH
rliterman@0: 
rliterman@0: RUN nucmer -h && \
rliterman@0:   promer -h && \
rliterman@0:   mummer -mum -b -c H_pylori26695_Eslice.fasta H_pyloriJ99_Eslice.fasta > mummer.mums && \
rliterman@0:   nucmer  -c 100 -p nucmer B_anthracis_Mslice.fasta B_anthracis_contigs.fasta && \
rliterman@0:   show-snps -C nucmer.delta > nucmer.snps && \
rliterman@0:   promer -p promer_100 -c 100  H_pylori26695_Eslice.fasta H_pyloriJ99_Eslice.fasta
rliterman@0: 
rliterman@0: # Test bedtools installation
rliterman@0: # check help options and version
rliterman@0: RUN bedtools --help && \
rliterman@0:     bedtools --version
rliterman@0: 
rliterman@0: # downloads two bedfiles for ARTIC SARS-CoV-2 artic schemes, fixes their formatting, uses bedtools sort, intersect, and merge
rliterman@0: # per https://github.com/StaPH-B/docker-builds/blob/master/bedtools/2.31.1/Dockerfile
rliterman@0: RUN awk '{print $1 "\t" $2 "\t" $3 "\t" $4 "\t" $5 "\t" $6}' V5.3.2.artic.bed > V5.3.2.unsorted.bed && \
rliterman@0:     bedtools sort -i V5.3.2.unsorted.bed > V5.3.2.bed && \
rliterman@0:     awk '{print $1 "\t" $2 "\t" $3 "\t" $4 "\t" $5 "\t" $6}' V4.1.artic.bed   > V4.1.bed   && \
rliterman@0:     bedtools intersect -a V5.3.2.bed -b V4.1.bed > intersect_test.bed && \
rliterman@0:     mergeBed -i V5.3.2.bed > merged_test.bed && \
rliterman@0:     head intersect_test.bed merged_test.bed
rliterman@0: 
rliterman@0: RUN /bin/bash -c 'make test'
rliterman@0: 
rliterman@0: FROM app AS release
rliterman@0: 
rliterman@0: ARG CSP2_VER
rliterman@0: ARG BEDTOOLS_VER
rliterman@0: ARG MUMMER_VER
rliterman@0: ARG SKESA_VER
rliterman@0: ARG MASH_VER
rliterman@0: ARG BBMAP_VER
rliterman@0: ARG PYTHON_VER
rliterman@0: ENV CSP2_VER=${CSP2_VER}
rliterman@0: ENV BEDTOOLS_VER=${BEDTOOLS_VER}
rliterman@0: ENV MUMMER_VER=${MUMMER_VER}
rliterman@0: ENV SKESA_VER=${SKESA_VER}
rliterman@0: ENV MASH_VER=${MASH_VER}
rliterman@0: ENV BBMAP_VER=${BBMAP_VER}
rliterman@0: ENV PYTHON_VER=${PYTHON_VER}
rliterman@0: 
rliterman@0: # set PATH, set perl locale settings for singularity compatibility
rliterman@0: ENV PATH="/opt/venv/bin:/usr/local/bin:/skesa:$PATH" \
rliterman@0:     LC_ALL=C \
rliterman@0:     NXF_OFFLINE='true'
rliterman@0: 
rliterman@0: ENTRYPOINT ["make", "--makefile=/app/Makefile"]