cfsan2snp2: Dockerfile annotate

annotate Dockerfile @ 10:ec50b4ed004c draft

planemo upload commit 73945687c1471741694cf99bbcdb8465ab5110f6

author	galaxytrakr
date	Thu, 19 Mar 2026 13:32:08 +0000
parents	0bf7e9b50206
children	2f515550dc87

rev	line source
0 8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	1 # =========================
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	2 # CSP2 for Galaxy/AWS Batch (offline Nextflow)
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	3 # =========================
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	4
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	5 # ---------- Build stage ----------
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	6 FROM ubuntu:focal AS build
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	7
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	8 ARG DEBIAN_FRONTEND=noninteractive
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	9 ARG CSP2_VER="0.9.0"
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	10 ARG BEDTOOLS_VER="2.31.1"
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	11 ARG MUMMER_VER="4.0.0"
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	12 ARG SKESA_VER="2.4.0"
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	13 ARG MASH_VER="2.3"
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	14 ARG BBMAP_VER="38.90"
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	15 ARG PYTHON_VER="3.8"
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	16 ARG SOURCEFORGE_MIRROR="psychz"
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	17 ARG IQTREE_VER="2.0.6"
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	18
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	19 # Use a stable working directory
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	20 WORKDIR /workspace
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	21
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	22 # Base build deps (include Java to verify/prewarm Nextflow here)
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	23 RUN apt-get update && apt-get install -y --no-install-recommends \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	24 tzdata gpg-agent software-properties-common build-essential \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	25 zlib1g-dev libghc-bzlib-dev liblzma-dev wget ca-certificates \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	26 cmake curl git xz-utils openjdk-17-jre-headless \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	27 && rm -rf /var/lib/apt/lists/*
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	28
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	29 # Python venv for runtime tools
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	30 RUN add-apt-repository 'ppa:deadsnakes/ppa' && apt-get update && \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	31 apt-get install -y --no-install-recommends \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	32 python${PYTHON_VER} python${PYTHON_VER}-dev python${PYTHON_VER}-venv \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	33 && python${PYTHON_VER} -m venv --copies /opt/venv \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	34 && rm -rf /var/lib/apt/lists/*
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	35
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	36 ENV PATH="/opt/venv/bin:${PATH}"
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	37
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	38 # Core Python packages
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	39 RUN pip install --no-cache-dir -U \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	40 pandas~=1.2.0 pybedtools refchooser scikit-learn
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	41
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	42 # ---- Fetch sources/artifacts ----
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	43 # bedtools
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	44 ADD https://github.com/arq5x/bedtools2/archive/refs/tags/v${BEDTOOLS_VER}.tar.gz .
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	45 # mummer
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	46 ADD https://github.com/mummer4/mummer/releases/download/v${MUMMER_VER}rc1/mummer-${MUMMER_VER}rc1.tar.gz .
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	47 # skesa prebuilt bins
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	48 ADD https://github.com/ncbi/SKESA/releases/download/${SKESA_VER}/skesa.centos.7.7 .
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	49 ADD https://github.com/ncbi/SKESA/releases/download/${SKESA_VER}/gfa_connector.centos7.7 .
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	50 ADD https://github.com/ncbi/SKESA/releases/download/${SKESA_VER}/kmercounter.centos7.7 .
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	51 # mash
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	52 ADD https://github.com/marbl/Mash/releases/download/v${MASH_VER}/mash-Linux64-v${MASH_VER}.tar .
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	53 # iqtree2
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	54 ADD https://github.com/Cibiv/IQ-TREE/releases/download/v${IQTREE_VER}/iqtree-${IQTREE_VER}-Linux.tar.gz .
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	55
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	56 # ---- Build/install tools into /usr/local ----
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	57 # bedtools
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	58 RUN tar -xzf v${BEDTOOLS_VER}.tar.gz && rm v${BEDTOOLS_VER}.tar.gz && \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	59 cd bedtools2-${BEDTOOLS_VER} && make -j && make install
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	60
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	61 # Install MUMmer and copy Perl modules where dnadiff expects them
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	62 RUN tar -xvf mummer-${MUMMER_VER}rc1.tar.gz && rm mummer-${MUMMER_VER}rc1.tar.gz && \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	63 cd mummer-${MUMMER_VER}rc1 && \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	64 ./configure --prefix=/usr/local && make -j && make install && ldconfig && \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	65 mkdir -p /usr/local/lib/mummer && cp -a scripts/*.pm /usr/local/lib/mummer/
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	66
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	67 # skesa tools (rename and install)
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	68 RUN install -m 0755 skesa.centos.7.7 /usr/local/bin/skesa && \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	69 install -m 0755 gfa_connector.centos7.7 /usr/local/bin/gfa_connector && \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	70 install -m 0755 kmercounter.centos7.7 /usr/local/bin/kmercounter
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	71
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	72 # mash
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	73 RUN tar -xvf mash-Linux64-v${MASH_VER}.tar && \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	74 install -m 0755 mash-Linux64-v${MASH_VER}/mash /usr/local/bin/mash
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	75
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	76 # bbmap (grab all scripts/binaries)
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	77 RUN wget -O BBMap_${BBMAP_VER}.tar.gz \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	78 "https://sourceforge.net/projects/bbmap/files/BBMap_${BBMAP_VER}.tar.gz/download?use_mirror=${SOURCEFORGE_MIRROR}" && \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	79 tar -xvf BBMap_${BBMAP_VER}.tar.gz && \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	80 cp -a bbmap/* /usr/local/bin/ && \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	81 rm -rf bbmap BBMap_${BBMAP_VER}.tar.gz
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	82
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	83 # iqtree2
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	84 RUN tar -xzf iqtree-${IQTREE_VER}-Linux.tar.gz && \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	85 install -m 0755 iqtree-${IQTREE_VER}-Linux/bin/iqtree2 /usr/local/bin/iqtree && \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	86 rm -rf iqtree-${IQTREE_VER}-Linux iqtree-${IQTREE_VER}-Linux.tar.gz
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	87
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	88 # choose a version
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	89 ARG NXF_VER="25.04.7"
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	90
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	91 # install that exact launcher & prewarm framework into /opt/nextflow
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	92 RUN curl -fsSL -o /usr/local/bin/nextflow \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	93 "https://github.com/nextflow-io/nextflow/releases/download/v${NXF_VER}/nextflow" \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	94 && chmod 0755 /usr/local/bin/nextflow \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	95 && mkdir -p /opt/nextflow \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	96 && chmod -R a+rwX /opt/nextflow \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	97 && NXF_HOME=/opt/nextflow NXF_OFFLINE=false NXF_VER=${NXF_VER} /usr/local/bin/nextflow -version \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	98 && ls -l /usr/local/bin/nextflow
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	99
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	100 # ---------- Runtime stage ----------
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	101 FROM ubuntu:focal AS runtime
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	102
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	103 ARG DEBIAN_FRONTEND=noninteractive
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	104 ARG CSP2_VER="0.9.0"
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	105
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	106 # Python venv for runtime tools
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	107 # Lean runtime libs + Python3.8 + Perl (no PPAs)
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	108 RUN apt-get update && apt-get install -y --no-install-recommends \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	109 ca-certificates openjdk-17-jre-headless bash tzdata perl perl-modules-5.30 \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	110 libgomp1 liblzma5 zlib1g libbz2-1.0 coreutils make curl gawk \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	111 python3.8 python3.8-venv python3.8-distutils \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	112 && rm -rf /var/lib/apt/lists/*
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	113
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	114 # Bring over tools and Python venv
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	115 COPY --from=build /usr/local/bin/ /usr/local/bin/
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	116 COPY --from=build /usr/local/libexec/mummer /usr/local/libexec/mummer
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	117 COPY --from=build /usr/local/share/ /usr/local/share/
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	118 COPY --from=build /opt/venv /opt/venv
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	119
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	120 # Bring over Nextflow launcher and baked framework cache
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	121 COPY --from=build /usr/local/bin/nextflow /usr/local/bin/nextflow
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	122 COPY --from=build /opt/nextflow /opt/nextflow
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	123
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	124 # Ensure any UID (Galaxy user) can execute nextflow and write minimal state into the cache
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	125 RUN chmod 0755 /usr/local/bin/nextflow \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	126 && chmod -R a+rwX /opt/nextflow
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	127
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	128 # Bring the modules into the runtime image (if not already)
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	129 COPY --from=build /usr/local/lib/mummer /usr/local/lib/mummer
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	130
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	131 # Bring MUMmer shared libs into the runtime image
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	132 COPY --from=build /usr/local/lib /usr/local/lib
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	133
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	134 # Make sure dynamic linker can find them
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	135 RUN ldconfig \|\| true
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	136
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	137 # Belt-and-suspenders for minimal images
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	138 ENV LD_LIBRARY_PATH="/usr/local/lib:${LD_LIBRARY_PATH}"
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	139
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	140 # Permissions: allow any UID to read/execute the libs
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	141 RUN chmod -R a+rX /usr/local/lib
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	142
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	143 # Make modules readable by any UID; create compatibility symlink if needed
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	144 RUN chmod -R a+rX /usr/local/lib/mummer /usr/local/libexec/mummer && \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	145 test -d /usr/local/lib/mummer \|\| ln -s /usr/local/libexec/mummer /usr/local/lib/mummer
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	146
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	147 # Ensure the common mummer executables are executable by all
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	148 RUN chmod 0755 /usr/local/bin/dnadiff /usr/local/bin/nucmer /usr/local/bin/promer /usr/local/bin/show-snps \|\| true
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	149
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	150 # Help Perl find modules regardless of layout
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	151 ENV PERL5LIB="/usr/local/lib/mummer:/usr/local/libexec/mummer:/usr/local/share/mummer:${PERL5LIB}"
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	152
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	153 # Runtime environment
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	154 ENV PATH="/opt/venv/bin:/usr/local/bin:${PATH}" \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	155 LC_ALL=C \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	156 NXF_HOME=/opt/nextflow \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	157 NXF_OFFLINE=true \
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	158 CSP2_VER=${CSP2_VER}
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	159
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	160 # Install the CSP2 pipeline under /opt/csp2 (avoid /app which Galaxy mounts)
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	161 WORKDIR /opt/csp2
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	162
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	163 # Copy your pipeline (these paths must exist in the build context)
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	164 COPY bin ./bin
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	165 COPY conf ./conf
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	166 COPY subworkflows ./subworkflows
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	167 COPY CSP2.nf ./CSP2.nf
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	168 COPY nextflow.config ./nextflow.config
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	169
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	170 # permissions for arbitrary UID
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	171 RUN chmod -R a+rX /opt/csp2 && chmod -R a+rX /opt/nextflow
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	172
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	173 # IMPORTANT: No ENTRYPOINT for Galaxy/AWS Batch. Neutral CMD.
8e7a84e62b43 planemo upload commit e734452c606dba89b6fe58c90c5f38e5ea067edd galaxytrakr parents: diff changeset	174 CMD ["/bin/bash"]

Mercurial > repos > galaxytrakr > cfsan2snp2

annotate Dockerfile @ 10:ec50b4ed004c draft