Mercurial > repos > rliterman > csp2

annotate CSP2/docker/Dockerfile @ 1:9df7494b1398

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload"
author rliterman
date Mon, 02 Dec 2024 11:24:02 -0500
parents 01431fa12065
children
rev   line source
rliterman@0 1 # CSP2 Dockerfile
rliterman@0 2 # Based on StaPH-B's Dockerfile for BEDTools, MUmmer, and Skesa
rliterman@0 3 # Thanks to Erin Young, Curtis Kapsak, John Arnn, and the StaPH-B team
rliterman@0 4 # https://github.com/StaPH-B/docker-builds/blob/master/bedtools/2.31.1/Dockerfile
rliterman@0 5 # https://github.com/StaPH-B/docker-builds/blob/master/mummer/4.0.0/Dockerfile
rliterman@0 6 # https://github.com/StaPH-B/docker-builds/blob/master/skesa/2.4.0/Dockerfile
rliterman@0 7
rliterman@0 8 ARG CSP2_VER="0.9.0"
rliterman@0 9 ARG BEDTOOLS_VER="2.31.1"
rliterman@0 10 ARG MUMMER_VER="4.0.0"
rliterman@0 11 ARG SKESA_VER="2.4.0"
rliterman@0 12 ARG MASH_VER="2.3"
rliterman@0 13 ARG BBMAP_VER="38.90"
rliterman@0 14 ARG PYTHON_VER="3.8"
rliterman@0 15
rliterman@0 16 FROM ubuntu:focal AS build
rliterman@0 17
rliterman@0 18 ARG BEDTOOLS_VER
rliterman@0 19 ARG MUMMER_VER
rliterman@0 20 ARG SKESA_VER
rliterman@0 21 ARG MASH_VER
rliterman@0 22 ARG BBMAP_VER
rliterman@0 23 ARG PYTHON_VER
rliterman@0 24
rliterman@0 25 WORKDIR /build
rliterman@0 26
rliterman@0 27 # to prevent tzdata from asking for a region during apt updates; ARG so that variable only
rliterman@0 28 # persists at buildtime
rliterman@0 29 # from https://github.com/StaPH-B/docker-builds/blob/master/mummer/4.0.0/Dockerfile
rliterman@0 30 ARG DEBIAN_FRONTEND=noninteractive
rliterman@0 31
rliterman@0 32 # Install build dependencies
rliterman@0 33 RUN apt-get update && apt-get install -y --no-install-recommends \
rliterman@0 34 tzdata \
rliterman@0 35 gpg-agent \
rliterman@0 36 software-properties-common \
rliterman@0 37 build-essential \
rliterman@0 38 zlib1g-dev \
rliterman@0 39 libghc-bzlib-dev \
rliterman@0 40 liblzma-dev \
rliterman@0 41 wget \
rliterman@0 42 ca-certificates
rliterman@0 43
rliterman@0 44 RUN add-apt-repository 'ppa:deadsnakes/ppa' && apt-get update && apt-get install -y --no-install-recommends \
rliterman@0 45 python${PYTHON_VER} \
rliterman@0 46 # python${PYTHON_VER}-pip \
rliterman@0 47 # python${PYTHON_VER}-full \
rliterman@0 48 python${PYTHON_VER}-dev \
rliterman@0 49 python${PYTHON_VER}-venv && \
rliterman@0 50 python${PYTHON_VER} -m venv --copies /opt/venv
rliterman@0 51
rliterman@0 52
rliterman@0 53 ENV PATH="/opt/venv/bin:$PATH"
rliterman@0 54
rliterman@0 55 RUN pip install --no-cache-dir -U pandas~=1.2.0 pybedtools refchooser scikit-learn
rliterman@0 56
rliterman@0 57 ADD https://github.com/arq5x/bedtools2/archive/refs/tags/v${BEDTOOLS_VER}.tar.gz .
rliterman@0 58 ADD https://github.com/mummer4/mummer/releases/download/v${MUMMER_VER}rc1/mummer-${MUMMER_VER}rc1.tar.gz .
rliterman@0 59 ADD https://github.com/ncbi/SKESA/releases/download/${SKESA_VER}/skesa.centos.7.7 .
rliterman@0 60 ADD https://github.com/ncbi/SKESA/releases/download/${SKESA_VER}/gfa_connector.centos7.7 .
rliterman@0 61 ADD https://github.com/ncbi/SKESA/releases/download/${SKESA_VER}/kmercounter.centos7.7 .
rliterman@0 62 ADD https://github.com/marbl/Mash/releases/download/v${MASH_VER}/mash-Linux64-v${MASH_VER}.tar .
rliterman@0 63
rliterman@0 64 # Install BEDTools
rliterman@0 65 # per https://github.com/StaPH-B/docker-builds/blob/master/bedtools/2.31.1/Dockerfile
rliterman@0 66 # python3 required when compiling via `make` command for creating old CLI executables
rliterman@0 67 # dependencies listed here (albeit for v2.30.0, still should be identical): https://packages.ubuntu.com/jammy/bedtools
rliterman@0 68 # requires libghc-bzlib-dev, build-essential, zlib1g-dev, and a few others
rliterman@0 69 # 'make install' should place binary executable files in /usr/local/bin
rliterman@0 70 RUN tar -xzf v${BEDTOOLS_VER}.tar.gz && \
rliterman@0 71 rm v${BEDTOOLS_VER}.tar.gz && \
rliterman@0 72 cd bedtools2-${BEDTOOLS_VER} && \
rliterman@0 73 make && \
rliterman@0 74 make install
rliterman@0 75
rliterman@0 76 # Install mummer
rliterman@0 77 # per https://github.com/StaPH-B/docker-builds/blob/master/mummer/4.0.0/Dockerfile
rliterman@0 78 RUN tar -xvf mummer-${MUMMER_VER}rc1.tar.gz && \
rliterman@0 79 rm mummer-${MUMMER_VER}rc1.tar.gz && \
rliterman@0 80 cd mummer-${MUMMER_VER}rc1 && \
rliterman@0 81 ./configure --prefix=/usr/local && \
rliterman@0 82 make && \
rliterman@0 83 make install && \
rliterman@0 84 ldconfig
rliterman@0 85
rliterman@0 86 # # Install Skesa
rliterman@0 87 # # per https://github.com/StaPH-B/docker-builds/blob/master/skesa/2.4.0/Dockerfile
rliterman@0 88 # # get skesa, gfa_connector, and kmercounter binaries, rename them
rliterman@0 89 RUN mkdir skesa && \
rliterman@0 90 cd skesa && \
rliterman@0 91 mv /build/skesa.centos.7.7 skesa && \
rliterman@0 92 mv /build/gfa_connector.centos7.7 gfa_connector && \
rliterman@0 93 mv /build/kmercounter.centos7.7 kmercounter && \
rliterman@0 94 chmod +x skesa gfa_connector kmercounter && \
rliterman@0 95 mv skesa gfa_connector kmercounter /usr/local/bin
rliterman@0 96
rliterman@0 97 # Install Mash
rliterman@0 98 RUN tar -xvf mash-Linux64-v${MASH_VER}.tar && \
rliterman@0 99 mv mash-Linux64-v${MASH_VER}/mash /usr/local/bin
rliterman@0 100
rliterman@0 101 # Install BBMap
rliterman@0 102 RUN wget -O BBMap_${BBMAP_VER}.tar.gz https://sourceforge.net/projects/bbmap/files/BBMap_${BBMAP_VER}.tar.gz/download && \
rliterman@0 103 tar -xvf BBMap_${BBMAP_VER}.tar.gz && \
rliterman@0 104 mv bbmap/* /usr/local/bin
rliterman@0 105
rliterman@0 106
rliterman@0 107 FROM ubuntu:focal AS app
rliterman@0 108
rliterman@0 109 ARG CSP2_VER
rliterman@0 110 ARG CSP2_BRANCH="main"
rliterman@0 111 ARG PYTHON_VER
rliterman@0 112
rliterman@0 113 LABEL base.image="ubuntu:focal"
rliterman@0 114 LABEL version=${CSP2_VER}
rliterman@0 115 LABEL software="CSP2"
rliterman@0 116 LABEL software.version=${CSP2_VER}
rliterman@0 117 LABEL description="a Nextflow pipeline for rapid, accurate SNP distance estimation from assembly data"
rliterman@0 118 LABEL website="https://github.com/CFSAN-Biostatistics/CSP2"
rliterman@0 119 LABEL licence="https://github.com/CFSAN-Biostatistics/CSP2/blob/main/LICENSE"
rliterman@0 120 LABEL maintainer="Robert Literman"
rliterman@0 121 LABEL maintainer.email="Robert.Literman@fda.hhs.gov"
rliterman@0 122 LABEL maintainer.organization="FDA/CFSAN/Biostatistics"
rliterman@0 123 LABEL maintainer2="Justin Payne"
rliterman@0 124 LABEL maintainer2.email="Justin.Payne@fda.hhs.gov"
rliterman@0 125 LABEL maintainer2.organization="FDA/CFSAN/Biostatistics"
rliterman@0 126
rliterman@0 127 WORKDIR /root/.nextflow
rliterman@0 128 WORKDIR /app
rliterman@0 129
rliterman@0 130 # copy in all executable files from builder stage to final app stage
rliterman@0 131 COPY --from=build /usr/local/bin /usr/local/bin
rliterman@0 132
rliterman@0 133 # Lots of perl nonsense
rliterman@0 134 COPY --from=build /usr/local/lib /usr/local/lib
rliterman@0 135 COPY --from=build /usr/local/libexec/mummer /usr/local/libexec/mummer
rliterman@0 136 COPY --from=build /usr/lib/x86_64-linux-gnu/perl /usr/lib/x86_64-linux-gnu/perl
rliterman@0 137 COPY --from=build /usr/local/share /usr/local/share
rliterman@0 138 COPY --from=build /usr/share /usr/share
rliterman@0 139 COPY --from=build /opt/venv /opt/venv
rliterman@0 140 COPY --from=build /usr/bin/make /usr/local/bin/make
rliterman@0 141
rliterman@0 142
rliterman@0 143 # Python stuff
rliterman@0 144 COPY --from=build /usr/lib/python${PYTHON_VER} /usr/lib/python${PYTHON_VER}
rliterman@0 145
rliterman@0 146
rliterman@0 147 #Install JRE
rliterman@0 148 RUN apt-get update && apt-get install -y --no-install-recommends \
rliterman@0 149 ca-certificates \
rliterman@0 150 openjdk-17-jre-headless \
rliterman@0 151 curl
rliterman@0 152
rliterman@0 153 # Install Nextflow
rliterman@0 154 # per https://www.nextflow.io/docs/latest/getstarted.html
rliterman@0 155 RUN export CAPSULE_LOG=debug && curl -s https://get.nextflow.io | bash && \
rliterman@0 156 chmod +x nextflow && \
rliterman@0 157 mv nextflow /usr/local/bin && \
rliterman@0 158 nextflow run hello
rliterman@0 159
rliterman@0 160 ADD docker/Makefile .
rliterman@0 161
rliterman@0 162 # set PATH, set perl locale settings for singularity compatibility
rliterman@0 163 ENV PATH="/opt/venv/bin:/usr/local/bin:/skesa:$PATH" \
rliterman@0 164 LC_ALL=C \
rliterman@0 165 NXF_OFFLINE='true'
rliterman@0 166
rliterman@0 167 ADD bin ./bin
rliterman@0 168 ADD conf ./conf
rliterman@0 169 ADD subworkflows ./subworkflows
rliterman@0 170 ADD CSP2.nf ./CSP2.nf
rliterman@0 171 ADD nextflow.config ./nextflow.config
rliterman@0 172
rliterman@0 173
rliterman@0 174 FROM app AS pretest
rliterman@0 175
rliterman@0 176 # set PATH, set perl locale settings for singularity compatibility
rliterman@0 177 ENV PATH="/opt/venv/bin:/usr/local/bin:/skesa:$PATH" \
rliterman@0 178 LC_ALL=C \
rliterman@0 179 NXF_OFFLINE='true'
rliterman@0 180
rliterman@0 181 #Alternate test data directory
rliterman@0 182 ADD https://github.com/CFSAN-Biostatistics/CSP2_TestData#main:assets assets/
rliterman@0 183
rliterman@0 184
rliterman@0 185 # Test MUmmer installation
rliterman@0 186 # per https://github.com/StaPH-B/docker-builds/blob/master/mummer/4.0.0/Dockerfile
rliterman@0 187
rliterman@0 188 ADD https://mummer4.github.io/tutorial/exampleFiles/2.1/in/H_pylori26695_Eslice.fasta .
rliterman@0 189 ADD https://mummer4.github.io/tutorial/exampleFiles/2.1/in/H_pyloriJ99_Eslice.fasta .
rliterman@0 190 ADD https://mummer4.github.io/tutorial/exampleFiles/2.2/in/B_anthracis_Mslice.fasta .
rliterman@0 191 ADD https://mummer4.github.io/tutorial/exampleFiles/2.2/in/B_anthracis_contigs.fasta .
rliterman@0 192 ADD http://mummer.sourceforge.net/examples/data/H_pylori26695_Eslice.fasta .
rliterman@0 193 ADD http://mummer.sourceforge.net/examples/data/H_pyloriJ99_Eslice.fasta .
rliterman@0 194 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@0 195 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@0 196
rliterman@0 197 FROM pretest AS test
rliterman@0 198
rliterman@0 199 # Test MASH
rliterman@0 200
rliterman@0 201 RUN nucmer -h && \
rliterman@0 202 promer -h && \
rliterman@0 203 mummer -mum -b -c H_pylori26695_Eslice.fasta H_pyloriJ99_Eslice.fasta > mummer.mums && \
rliterman@0 204 nucmer -c 100 -p nucmer B_anthracis_Mslice.fasta B_anthracis_contigs.fasta && \
rliterman@0 205 show-snps -C nucmer.delta > nucmer.snps && \
rliterman@0 206 promer -p promer_100 -c 100 H_pylori26695_Eslice.fasta H_pyloriJ99_Eslice.fasta
rliterman@0 207
rliterman@0 208 # Test bedtools installation
rliterman@0 209 # check help options and version
rliterman@0 210 RUN bedtools --help && \
rliterman@0 211 bedtools --version
rliterman@0 212
rliterman@0 213 # downloads two bedfiles for ARTIC SARS-CoV-2 artic schemes, fixes their formatting, uses bedtools sort, intersect, and merge
rliterman@0 214 # per https://github.com/StaPH-B/docker-builds/blob/master/bedtools/2.31.1/Dockerfile
rliterman@0 215 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@0 216 bedtools sort -i V5.3.2.unsorted.bed > V5.3.2.bed && \
rliterman@0 217 awk '{print $1 "\t" $2 "\t" $3 "\t" $4 "\t" $5 "\t" $6}' V4.1.artic.bed > V4.1.bed && \
rliterman@0 218 bedtools intersect -a V5.3.2.bed -b V4.1.bed > intersect_test.bed && \
rliterman@0 219 mergeBed -i V5.3.2.bed > merged_test.bed && \
rliterman@0 220 head intersect_test.bed merged_test.bed
rliterman@0 221
rliterman@0 222 RUN /bin/bash -c 'make test'
rliterman@0 223
rliterman@0 224 FROM app AS release
rliterman@0 225
rliterman@0 226 ARG CSP2_VER
rliterman@0 227 ARG BEDTOOLS_VER
rliterman@0 228 ARG MUMMER_VER
rliterman@0 229 ARG SKESA_VER
rliterman@0 230 ARG MASH_VER
rliterman@0 231 ARG BBMAP_VER
rliterman@0 232 ARG PYTHON_VER
rliterman@0 233 ENV CSP2_VER=${CSP2_VER}
rliterman@0 234 ENV BEDTOOLS_VER=${BEDTOOLS_VER}
rliterman@0 235 ENV MUMMER_VER=${MUMMER_VER}
rliterman@0 236 ENV SKESA_VER=${SKESA_VER}
rliterman@0 237 ENV MASH_VER=${MASH_VER}
rliterman@0 238 ENV BBMAP_VER=${BBMAP_VER}
rliterman@0 239 ENV PYTHON_VER=${PYTHON_VER}
rliterman@0 240
rliterman@0 241 # set PATH, set perl locale settings for singularity compatibility
rliterman@0 242 ENV PATH="/opt/venv/bin:/usr/local/bin:/skesa:$PATH" \
rliterman@0 243 LC_ALL=C \
rliterman@0 244 NXF_OFFLINE='true'
rliterman@0 245
rliterman@0 246 ENTRYPOINT ["make", "--makefile=/app/Makefile"]