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+++ b/CSP2/docker/Dockerfile	Thu Dec 12 13:53:15 2024 -0500
@@ -0,0 +1,246 @@
+# CSP2 Dockerfile
+# Based on StaPH-B's Dockerfile for BEDTools, MUmmer, and Skesa
+# Thanks to Erin Young, Curtis Kapsak, John Arnn, and the StaPH-B team
+# https://github.com/StaPH-B/docker-builds/blob/master/bedtools/2.31.1/Dockerfile
+# https://github.com/StaPH-B/docker-builds/blob/master/mummer/4.0.0/Dockerfile
+# https://github.com/StaPH-B/docker-builds/blob/master/skesa/2.4.0/Dockerfile
+
+ARG CSP2_VER="0.9.0"
+ARG BEDTOOLS_VER="2.31.1"
+ARG MUMMER_VER="4.0.0"
+ARG SKESA_VER="2.4.0"
+ARG MASH_VER="2.3"
+ARG BBMAP_VER="38.90"
+ARG PYTHON_VER="3.8"
+
+FROM ubuntu:focal AS build
+
+ARG BEDTOOLS_VER
+ARG MUMMER_VER
+ARG SKESA_VER
+ARG MASH_VER
+ARG BBMAP_VER
+ARG PYTHON_VER
+
+WORKDIR /build
+
+# to prevent tzdata from asking for a region during apt updates; ARG so that variable only 
+# persists at buildtime
+# from https://github.com/StaPH-B/docker-builds/blob/master/mummer/4.0.0/Dockerfile
+ARG DEBIAN_FRONTEND=noninteractive
+
+# Install build dependencies
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    tzdata \
+    gpg-agent \
+    software-properties-common \
+    build-essential \
+    zlib1g-dev \
+    libghc-bzlib-dev \
+    liblzma-dev \
+    wget \
+    ca-certificates 
+
+RUN add-apt-repository 'ppa:deadsnakes/ppa' && apt-get update && apt-get install -y --no-install-recommends \
+    python${PYTHON_VER} \
+#    python${PYTHON_VER}-pip \
+#    python${PYTHON_VER}-full \
+    python${PYTHON_VER}-dev \
+    python${PYTHON_VER}-venv && \
+    python${PYTHON_VER} -m venv --copies /opt/venv
+
+
+ENV PATH="/opt/venv/bin:$PATH"
+
+RUN pip install --no-cache-dir -U pandas~=1.2.0 pybedtools refchooser scikit-learn
+
+ADD https://github.com/arq5x/bedtools2/archive/refs/tags/v${BEDTOOLS_VER}.tar.gz .
+ADD https://github.com/mummer4/mummer/releases/download/v${MUMMER_VER}rc1/mummer-${MUMMER_VER}rc1.tar.gz .
+ADD https://github.com/ncbi/SKESA/releases/download/${SKESA_VER}/skesa.centos.7.7 .
+ADD https://github.com/ncbi/SKESA/releases/download/${SKESA_VER}/gfa_connector.centos7.7 .
+ADD https://github.com/ncbi/SKESA/releases/download/${SKESA_VER}/kmercounter.centos7.7 .
+ADD https://github.com/marbl/Mash/releases/download/v${MASH_VER}/mash-Linux64-v${MASH_VER}.tar .
+
+# Install BEDTools
+# per https://github.com/StaPH-B/docker-builds/blob/master/bedtools/2.31.1/Dockerfile
+# python3 required when compiling via `make` command for creating old CLI executables
+# dependencies listed here (albeit for v2.30.0, still should be identical): https://packages.ubuntu.com/jammy/bedtools
+# requires libghc-bzlib-dev, build-essential, zlib1g-dev, and a few others
+# 'make install' should place binary executable files in /usr/local/bin
+RUN tar -xzf v${BEDTOOLS_VER}.tar.gz && \
+    rm v${BEDTOOLS_VER}.tar.gz && \
+   cd bedtools2-${BEDTOOLS_VER} && \
+   make && \
+   make install 
+
+ # Install mummer
+ # per https://github.com/StaPH-B/docker-builds/blob/master/mummer/4.0.0/Dockerfile
+RUN tar -xvf mummer-${MUMMER_VER}rc1.tar.gz && \
+    rm mummer-${MUMMER_VER}rc1.tar.gz && \
+    cd mummer-${MUMMER_VER}rc1 && \
+    ./configure --prefix=/usr/local && \
+    make && \
+    make install && \
+    ldconfig
+
+# # Install Skesa
+# # per https://github.com/StaPH-B/docker-builds/blob/master/skesa/2.4.0/Dockerfile
+# # get skesa, gfa_connector, and kmercounter binaries, rename them
+RUN mkdir skesa && \
+    cd skesa && \
+    mv /build/skesa.centos.7.7 skesa && \
+    mv /build/gfa_connector.centos7.7 gfa_connector && \
+    mv /build/kmercounter.centos7.7 kmercounter && \
+    chmod +x skesa gfa_connector kmercounter && \
+    mv skesa gfa_connector kmercounter /usr/local/bin
+
+# Install Mash
+RUN tar -xvf mash-Linux64-v${MASH_VER}.tar && \
+    mv mash-Linux64-v${MASH_VER}/mash /usr/local/bin
+
+# Install BBMap
+RUN wget -O BBMap_${BBMAP_VER}.tar.gz https://sourceforge.net/projects/bbmap/files/BBMap_${BBMAP_VER}.tar.gz/download && \
+    tar -xvf BBMap_${BBMAP_VER}.tar.gz && \
+    mv bbmap/* /usr/local/bin
+
+
+FROM ubuntu:focal AS app
+
+ARG CSP2_VER
+ARG CSP2_BRANCH="main"
+ARG PYTHON_VER
+
+LABEL base.image="ubuntu:focal"
+LABEL version=${CSP2_VER}
+LABEL software="CSP2"
+LABEL software.version=${CSP2_VER}
+LABEL description="a Nextflow pipeline for rapid, accurate SNP distance estimation from assembly data"
+LABEL website="https://github.com/CFSAN-Biostatistics/CSP2"
+LABEL licence="https://github.com/CFSAN-Biostatistics/CSP2/blob/main/LICENSE"
+LABEL maintainer="Robert Literman"
+LABEL maintainer.email="Robert.Literman@fda.hhs.gov"
+LABEL maintainer.organization="FDA/CFSAN/Biostatistics"
+LABEL maintainer2="Justin Payne"
+LABEL maintainer2.email="Justin.Payne@fda.hhs.gov"
+LABEL maintainer2.organization="FDA/CFSAN/Biostatistics"
+
+WORKDIR /root/.nextflow
+WORKDIR /app
+
+# copy in all executable files from builder stage to final app stage
+COPY --from=build /usr/local/bin /usr/local/bin
+
+# Lots of perl nonsense
+COPY --from=build /usr/local/lib /usr/local/lib
+COPY --from=build /usr/local/libexec/mummer /usr/local/libexec/mummer
+COPY --from=build /usr/lib/x86_64-linux-gnu/perl /usr/lib/x86_64-linux-gnu/perl
+COPY --from=build /usr/local/share /usr/local/share
+COPY --from=build /usr/share /usr/share
+COPY --from=build /opt/venv /opt/venv
+COPY --from=build /usr/bin/make /usr/local/bin/make
+
+
+# Python stuff
+COPY --from=build /usr/lib/python${PYTHON_VER} /usr/lib/python${PYTHON_VER}
+
+
+#Install JRE
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    ca-certificates \
+    openjdk-17-jre-headless \
+    curl
+
+# Install Nextflow
+# per https://www.nextflow.io/docs/latest/getstarted.html
+RUN export CAPSULE_LOG=debug && curl -s https://get.nextflow.io | bash && \
+    chmod +x nextflow && \
+    mv nextflow /usr/local/bin && \
+    nextflow run hello
+
+ADD docker/Makefile .
+
+# set PATH, set perl locale settings for singularity compatibility
+ENV PATH="/opt/venv/bin:/usr/local/bin:/skesa:$PATH" \
+    LC_ALL=C \
+    NXF_OFFLINE='true'
+
+ADD bin ./bin
+ADD conf ./conf
+ADD subworkflows ./subworkflows
+ADD CSP2.nf ./CSP2.nf
+ADD nextflow.config ./nextflow.config
+
+
+FROM app AS pretest
+
+# set PATH, set perl locale settings for singularity compatibility
+ENV PATH="/opt/venv/bin:/usr/local/bin:/skesa:$PATH" \
+    LC_ALL=C \
+    NXF_OFFLINE='true'
+
+#Alternate test data directory
+ADD https://github.com/CFSAN-Biostatistics/CSP2_TestData#main:assets assets/
+
+
+# Test MUmmer installation
+# per https://github.com/StaPH-B/docker-builds/blob/master/mummer/4.0.0/Dockerfile
+
+ADD https://mummer4.github.io/tutorial/exampleFiles/2.1/in/H_pylori26695_Eslice.fasta .
+ADD https://mummer4.github.io/tutorial/exampleFiles/2.1/in/H_pyloriJ99_Eslice.fasta .
+ADD https://mummer4.github.io/tutorial/exampleFiles/2.2/in/B_anthracis_Mslice.fasta .
+ADD https://mummer4.github.io/tutorial/exampleFiles/2.2/in/B_anthracis_contigs.fasta .
+ADD http://mummer.sourceforge.net/examples/data/H_pylori26695_Eslice.fasta .
+ADD http://mummer.sourceforge.net/examples/data/H_pyloriJ99_Eslice.fasta .
+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
+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
+
+FROM pretest AS test
+
+# Test MASH
+
+RUN nucmer -h && \
+  promer -h && \
+  mummer -mum -b -c H_pylori26695_Eslice.fasta H_pyloriJ99_Eslice.fasta > mummer.mums && \
+  nucmer  -c 100 -p nucmer B_anthracis_Mslice.fasta B_anthracis_contigs.fasta && \
+  show-snps -C nucmer.delta > nucmer.snps && \
+  promer -p promer_100 -c 100  H_pylori26695_Eslice.fasta H_pyloriJ99_Eslice.fasta
+
+# Test bedtools installation
+# check help options and version
+RUN bedtools --help && \
+    bedtools --version
+
+# downloads two bedfiles for ARTIC SARS-CoV-2 artic schemes, fixes their formatting, uses bedtools sort, intersect, and merge
+# per https://github.com/StaPH-B/docker-builds/blob/master/bedtools/2.31.1/Dockerfile
+RUN awk '{print $1 "\t" $2 "\t" $3 "\t" $4 "\t" $5 "\t" $6}' V5.3.2.artic.bed > V5.3.2.unsorted.bed && \
+    bedtools sort -i V5.3.2.unsorted.bed > V5.3.2.bed && \
+    awk '{print $1 "\t" $2 "\t" $3 "\t" $4 "\t" $5 "\t" $6}' V4.1.artic.bed   > V4.1.bed   && \
+    bedtools intersect -a V5.3.2.bed -b V4.1.bed > intersect_test.bed && \
+    mergeBed -i V5.3.2.bed > merged_test.bed && \
+    head intersect_test.bed merged_test.bed
+
+RUN /bin/bash -c 'make test'
+
+FROM app AS release
+
+ARG CSP2_VER
+ARG BEDTOOLS_VER
+ARG MUMMER_VER
+ARG SKESA_VER
+ARG MASH_VER
+ARG BBMAP_VER
+ARG PYTHON_VER
+ENV CSP2_VER=${CSP2_VER}
+ENV BEDTOOLS_VER=${BEDTOOLS_VER}
+ENV MUMMER_VER=${MUMMER_VER}
+ENV SKESA_VER=${SKESA_VER}
+ENV MASH_VER=${MASH_VER}
+ENV BBMAP_VER=${BBMAP_VER}
+ENV PYTHON_VER=${PYTHON_VER}
+
+# set PATH, set perl locale settings for singularity compatibility
+ENV PATH="/opt/venv/bin:/usr/local/bin:/skesa:$PATH" \
+    LC_ALL=C \
+    NXF_OFFLINE='true'
+
+ENTRYPOINT ["make", "--makefile=/app/Makefile"]
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