Add IsoSeq images #21
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| FROM ubuntu:focal | ||
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| MAINTAINER Heather Ward <heather@dnastack.com> | ||
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| ARG IMAGE_NAME | ||
| ENV IMAGE_NAME "${IMAGE_NAME}" | ||
| ARG IMAGE_TAG | ||
| ENV IMAGE_TAG "${IMAGE_TAG}" | ||
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| RUN apt-get -qq update \ | ||
| && apt-get -qq install \ | ||
| wget \ | ||
| && rm -rf /var/lib/apt/lists/* | ||
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| ARG ISOSEQ_VERSION | ||
| RUN wget https://github.com/PacificBiosciences/IsoSeq/releases/download/v${ISOSEQ_VERSION}/isoseq --directory-prefix /opt/isoseq \ | ||
| && chmod +x /opt/isoseq/isoseq \ | ||
| && ln -s /opt/isoseq/isoseq /usr/local/bin |
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| # Tool versions | ||
| ISOSEQ_VERSION=4.0.0 | ||
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| # Image info | ||
| IMAGE_NAME=isoseq | ||
| IMAGE_TAG=${ISOSEQ_VERSION} |
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| FROM ubuntu:focal | ||
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| MAINTAINER Heather Ward <heather@dnastack.com> | ||
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| ARG IMAGE_NAME | ||
| ENV IMAGE_NAME "${IMAGE_NAME}" | ||
| ARG IMAGE_TAG | ||
| ENV IMAGE_TAG "${IMAGE_TAG}" | ||
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| RUN apt-get -qq update \ | ||
| && apt-get -qq install \ | ||
| wget \ | ||
| && rm -rf /var/lib/apt/lists/* | ||
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| # Need to explicitly grant executable to non-root users | ||
| ARG LIMA_VERSION | ||
| RUN wget https://github.com/PacificBiosciences/barcoding/releases/download/v${LIMA_VERSION}/lima.tar.gz \ | ||
| && mkdir /opt/lima \ | ||
| && tar -zxvf lima.tar.gz --directory /opt/lima \ | ||
| && rm lima.tar.gz \ | ||
| && chmod +x /opt/lima/* | ||
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| ENV PATH ${PATH}:/opt/lima |
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| # Tool versions | ||
| LIMA_VERSION=2.7.1 | ||
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| # Image info | ||
| IMAGE_NAME=lima | ||
| IMAGE_TAG=${LIMA_VERSION} |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,85 @@ | ||
| FROM ubuntu:jammy | ||
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| MAINTAINER Heather Ward <heather@dnastack.com> | ||
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| ARG IMAGE_NAME | ||
| ENV IMAGE_NAME "${IMAGE_NAME}" | ||
| ARG IMAGE_TAG | ||
| ENV IMAGE_TAG "${IMAGE_TAG}" | ||
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| ENV DEBIAN_FRONTEND noninteractive | ||
| RUN apt-get -qq update \ | ||
| && apt-get -qq install \ | ||
| wget \ | ||
| unzip \ | ||
| python2-dev \ | ||
| python3-dev \ | ||
| python3-pip \ | ||
| zlib1g-dev \ | ||
| libncurses5-dev \ | ||
| liblzma-dev \ | ||
| libbz2-dev \ | ||
| libcurl4-openssl-dev \ | ||
| libgtest-dev \ | ||
| pkg-config \ | ||
| git \ | ||
| cmake \ | ||
| && rm -rf /var/lib/apt/lists/* | ||
| RUN update-alternatives --install /usr/bin/python python /usr/bin/python2 2 | ||
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| # Need bash for curly brace pattern replace for boost version | ||
| SHELL ["/bin/bash", "-c"] | ||
| ARG BOOST_VERSION | ||
| RUN wget https://boostorg.jfrog.io/artifactory/main/release/${BOOST_VERSION}/source/boost_${BOOST_VERSION//./_}.tar.gz \ | ||
| && tar -zxvf boost_${BOOST_VERSION//./_}.tar.gz --directory /opt \ | ||
| && rm boost_${BOOST_VERSION//./_}.tar.gz | ||
| RUN cd /opt/boost_${BOOST_VERSION//./_} \ | ||
| && ./bootstrap.sh \ | ||
| && ./b2 \ | ||
| && ./b2 headers \ | ||
| && ./b2 install | ||
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| ARG MESON_VERSION | ||
| RUN python3 -m pip install meson==${MESON_VERSION} cram | ||
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| ARG HTSLIB_VERSION | ||
| RUN wget https://github.com/samtools/htslib/releases/download/${HTSLIB_VERSION}/htslib-${HTSLIB_VERSION}.tar.bz2 \ | ||
| && tar -jxvf htslib-${HTSLIB_VERSION}.tar.bz2 --directory /opt \ | ||
| && rm htslib-${HTSLIB_VERSION}.tar.bz2 | ||
| RUN cd /opt/htslib-${HTSLIB_VERSION} \ | ||
| && make \ | ||
| && make install | ||
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| ARG SAMTOOLS_VERSION | ||
| RUN wget https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2 \ | ||
| && tar -jxvf samtools-${SAMTOOLS_VERSION}.tar.bz2 --directory /opt \ | ||
| && rm samtools-${SAMTOOLS_VERSION}.tar.bz2 | ||
| RUN cd /opt/samtools-${SAMTOOLS_VERSION} \ | ||
| && make \ | ||
| && make install | ||
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| ARG NINJA_VERSION | ||
| RUN mkdir /opt/ninja \ | ||
| && wget https://github.com/ninja-build/ninja/releases/download/v${NINJA_VERSION}/ninja-linux.zip \ | ||
| && unzip -d /opt/ninja ninja-linux.zip \ | ||
| && rm ninja-linux.zip \ | ||
| && ln -s /opt/ninja/ninja /usr/local/bin/ninja | ||
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| ARG PBCOPPER_VERSION | ||
| RUN wget https://github.com/PacificBiosciences/pbcopper/archive/refs/tags/v${PBCOPPER_VERSION}.tar.gz \ | ||
| && tar -zxvf v${PBCOPPER_VERSION}.tar.gz --directory /opt \ | ||
| && rm v${PBCOPPER_VERSION}.tar.gz | ||
| RUN cd /opt/pbcopper-${PBCOPPER_VERSION} \ | ||
| && meson build . \ | ||
| && cd build \ | ||
| && meson install | ||
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| ARG PBBAM_VERSION | ||
| RUN wget https://github.com/PacificBiosciences/pbbam/archive/refs/tags/v${PBBAM_VERSION}.tar.gz \ | ||
| && tar -zxvf v${PBBAM_VERSION}.tar.gz --directory /opt \ | ||
| && rm v${PBBAM_VERSION}.tar.gz | ||
| RUN cd /opt/pbbam-${PBBAM_VERSION} \ | ||
| && meson build . \ | ||
| && meson install -C build | ||
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| ENV LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/usr/local/lib:/usr/local/lib/x86_64-linux-gnu/ |
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| # Tool versions | ||
| PBBAM_VERSION=2.3.0 | ||
| BOOST_VERSION=1.82.0 | ||
| MESON_VERSION=0.57.0 | ||
| HTSLIB_VERSION=1.17 | ||
| SAMTOOLS_VERSION=1.17 | ||
| NINJA_VERSION=1.11.1 | ||
| PBCOPPER_VERSION=2.2.0 | ||
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| # Image info | ||
| IMAGE_NAME=pbbam | ||
| IMAGE_TAG=${PBBAM_VERSION} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,18 @@ | ||
| FROM ubuntu:jammy | ||
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| MAINTAINER Heather Ward <heather@dnastack.com> | ||
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| ARG IMAGE_NAME | ||
| ENV IMAGE_NAME "${IMAGE_NAME}" | ||
| ARG IMAGE_TAG | ||
| ENV IMAGE_TAG "${IMAGE_TAG}" | ||
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| RUN apt-get -qq update \ | ||
| && apt-get -qq install \ | ||
| wget \ | ||
| && rm -rf /var/lib/apt/lists/* | ||
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| ARG PIGEON_VERSION | ||
| RUN wget https://github.com/PacificBiosciences/pigeon/releases/download/v${PIGEON_VERSION}/pigeon --directory-prefix /opt/pigeon \ | ||
| && chmod +x /opt/pigeon/pigeon \ | ||
| && ln -s /opt/pigeon/pigeon /usr/local/bin |
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| @@ -0,0 +1,6 @@ | ||
| # Tool versions | ||
| PIGEON_VERSION=1.1.0 | ||
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| # Image info | ||
| IMAGE_NAME=pigeon | ||
| IMAGE_TAG=${PIGEON_VERSION} |
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Collaborator
There was a problem hiding this comment. samtools/isoseq and samtools/humanwgs are the same, except for version. We could probably get away with a single image to support both. We just need to test the new version within the context of wdl-humanwgs. |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,27 @@ | ||
| FROM ubuntu:focal | ||
|
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| MAINTAINER Heather Ward <heather@dnastack.com> | ||
|
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| ARG IMAGE_NAME | ||
| ENV IMAGE_NAME "${IMAGE_NAME}" | ||
| ARG IMAGE_TAG | ||
| ENV IMAGE_TAG "${IMAGE_TAG}" | ||
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| RUN apt-get -qq update \ | ||
| && apt-get -qq install \ | ||
| wget \ | ||
| build-essential \ | ||
| zlib1g-dev \ | ||
| libncurses5-dev \ | ||
| liblzma-dev \ | ||
| libbz2-dev \ | ||
| libcurl4-openssl-dev \ | ||
| && rm -rf /var/lib/apt/lists/* | ||
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| ARG SAMTOOLS_VERSION | ||
| RUN wget https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2 \ | ||
| && tar -jxvf samtools-${SAMTOOLS_VERSION}.tar.bz2 --directory /opt \ | ||
| && rm samtools-${SAMTOOLS_VERSION}.tar.bz2 | ||
| RUN cd /opt/samtools-${SAMTOOLS_VERSION} \ | ||
| && make \ | ||
| && make install |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| # Tool versions | ||
| SAMTOOLS_VERSION=1.17 | ||
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| # Image info | ||
| IMAGE_NAME=samtools | ||
| IMAGE_TAG=${SAMTOOLS_VERSION} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,18 @@ | ||
| FROM ubuntu:focal | ||
|
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| MAINTAINER Heather Ward <heather@dnastack.com> | ||
|
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| ARG IMAGE_NAME | ||
| ENV IMAGE_NAME "${IMAGE_NAME}" | ||
| ARG IMAGE_TAG | ||
| ENV IMAGE_TAG "${IMAGE_TAG}" | ||
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| RUN apt-get -qq update \ | ||
| && apt-get -qq install \ | ||
| wget \ | ||
| && rm -rf /var/lib/apt/lists/* | ||
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| ARG SKERA_VERSION | ||
| RUN wget https://github.com/PacificBiosciences/skera/releases/download/v${SKERA_VERSION}/skera --directory-prefix /opt/skera \ | ||
| && chmod +x /opt/skera/skera \ | ||
| && ln -s /opt/skera/skera /usr/local/bin |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| # Tool versions | ||
| SKERA_VERSION=1.1.0 | ||
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| # Image info | ||
| IMAGE_NAME=skera | ||
| IMAGE_TAG=${SKERA_VERSION} |
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As far as I can tell, the difference between lima/isoseq and lima/targetenrichment is just lima version. 2.5 vs 2.7. Maybe worth checking whether the newest is compatible with both?