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Merge pull request #904 from StaPH-B/cjk-pdata-1.26
Adds pangolin 4.3.1 with new version of pangolin-data v1.26
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| FROM mambaorg/micromamba:1.5.7 as app | ||
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| # build and run as root users since micromamba image has 'mambauser' set as the $USER | ||
| USER root | ||
| # set workdir to default for building; set to /data at the end | ||
| WORKDIR / | ||
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| # ARG variables only persist during build time | ||
| # had to include the v for some of these due to GitHub tags. | ||
| # using pangolin-data github tag, NOT what is in the GH release title "v1.2.133" | ||
| ARG PANGOLIN_VER="v4.3.1" | ||
| ARG PANGOLIN_DATA_VER="v1.26" | ||
| ARG SCORPIO_VER="v0.3.19" | ||
| ARG CONSTELLATIONS_VER="v0.1.12" | ||
| ARG USHER_VER="0.6.3" | ||
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| # metadata labels | ||
| LABEL base.image="mambaorg/micromamba:1.5.7" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="pangolin" | ||
| LABEL software.version=${PANGOLIN_VER} | ||
| LABEL description="Conda environment for Pangolin. Pangolin: Software package for assigning SARS-CoV-2 genome sequences to global lineages." | ||
| LABEL website="https://github.com/cov-lineages/pangolin" | ||
| LABEL license="GNU General Public License v3.0" | ||
| LABEL license.url="https://github.com/cov-lineages/pangolin/blob/master/LICENSE.txt" | ||
| LABEL maintainer="Curtis Kapsak" | ||
| LABEL maintainer.email="[email protected]" | ||
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| # install dependencies; cleanup apt garbage | ||
| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| wget \ | ||
| ca-certificates \ | ||
| git \ | ||
| procps \ | ||
| bsdmainutils && \ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
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| # get the pangolin repo | ||
| RUN wget "https://github.com/cov-lineages/pangolin/archive/${PANGOLIN_VER}.tar.gz" && \ | ||
| tar -xf ${PANGOLIN_VER}.tar.gz && \ | ||
| rm -v ${PANGOLIN_VER}.tar.gz && \ | ||
| mv -v pangolin-* pangolin | ||
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| # set the environment; PATH is unnecessary here, but leaving anyways. It's reset later in dockerfile | ||
| ENV PATH="$PATH" \ | ||
| LC_ALL=C.UTF-8 | ||
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| # modify environment.yml to pin specific versions during install | ||
| # pin specific versions of usher, scorpio, pangolin-data, constellations, and pulp | ||
| # create the conda environment using modified environment.yml | ||
| RUN sed -i "s|usher.*|usher=${USHER_VER}|" /pangolin/environment.yml && \ | ||
| sed -i "s|scorpio.git|scorpio.git@${SCORPIO_VER}|" /pangolin/environment.yml && \ | ||
| sed -i "s|pangolin-data.git|pangolin-data.git@${PANGOLIN_DATA_VER}|" /pangolin/environment.yml && \ | ||
| sed -i "s|constellations.git|constellations.git@${CONSTELLATIONS_VER}|" /pangolin/environment.yml && \ | ||
| sed -i "12 a\ - pulp=2.7.0" /pangolin/environment.yml && \ | ||
| micromamba create -n pangolin -y -f /pangolin/environment.yml | ||
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| # so that mamba/conda env is active when running below commands | ||
| ENV ENV_NAME="pangolin" | ||
| ARG MAMBA_DOCKERFILE_ACTIVATE=1 | ||
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| WORKDIR /pangolin | ||
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| # run pip install step; download optional pre-computed assignment hashes for UShER (useful for running on large batches of samples) | ||
| # best to skip using the assigment-cache if running on one sample for speed | ||
| # print versions | ||
| RUN pip install . && \ | ||
| pangolin --add-assignment-cache && \ | ||
| micromamba clean -a -y && \ | ||
| mkdir /data && \ | ||
| pangolin --all-versions && \ | ||
| usher --version | ||
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| # final working directory in "app" layer is /data for passing data in/out of container | ||
| WORKDIR /data | ||
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| # hardcode pangolin executable into the PATH variable | ||
| ENV PATH="${PATH}:/opt/conda/envs/pangolin/bin/" XDG_CACHE_HOME=/tmp | ||
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| # default command is to pull up help options for pangolin; can be overridden of course | ||
| CMD ["pangolin", "-h"] | ||
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| # new base for testing | ||
| FROM app as test | ||
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| # so that mamba/conda env is active when running below commands | ||
| ENV ENV_NAME="pangolin" | ||
| ARG MAMBA_DOCKERFILE_ACTIVATE=1 | ||
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| # test on test sequences supplied with Pangolin code | ||
| RUN pangolin /pangolin/pangolin/test/test_seqs.fasta -o /data/test_seqs-output-pusher && \ | ||
| column -t -s, /data/test_seqs-output-pusher/lineage_report.csv | ||
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| # test functionality of assignment-cache option | ||
| RUN pangolin --use-assignment-cache /pangolin/pangolin/test/test_seqs.fasta | ||
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| # download B.1.1.7 genome from Utah | ||
| ADD https://raw.githubusercontent.com/StaPH-B/docker-builds/master/tests/SARS-CoV-2/SRR13957123.consensus.fa /test-data/SRR13957123.consensus.fa | ||
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| # test on a B.1.1.7 genome | ||
| RUN pangolin /test-data/SRR13957123.consensus.fa -o /test-data/SRR13957123-pusher && \ | ||
| column -t -s, /test-data/SRR13957123-pusher/lineage_report.csv | ||
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| # install unzip for unzipping zip archive from NCBI | ||
| RUN apt-get update && apt-get install -y --no-install-recommends unzip | ||
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| # install ncbi datasets tool (pre-compiled binary); place in $PATH | ||
| RUN wget https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/LATEST/linux-amd64/datasets && \ | ||
| chmod +x datasets && \ | ||
| mv -v datasets /usr/local/bin | ||
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| # download assembly for a BA.1 from Florida (https://www.ncbi.nlm.nih.gov/biosample?term=SAMN29506515 and https://www.ncbi.nlm.nih.gov/nuccore/ON924087) | ||
| # run pangolin in usher analysis mode | ||
| RUN datasets download virus genome accession ON924087.1 --filename ON924087.1.zip && \ | ||
| unzip ON924087.1.zip && rm ON924087.1.zip && \ | ||
| mv -v ncbi_dataset/data/genomic.fna ON924087.1.genomic.fna && \ | ||
| rm -vr ncbi_dataset/ README.md && \ | ||
| pangolin ON924087.1.genomic.fna -o ON924087.1-usher && \ | ||
| column -t -s, ON924087.1-usher/lineage_report.csv | ||
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| # test specific for new lineage, XBB.1.16, introduced in pangolin-data v1.19 | ||
| # using this assembly: https://www.ncbi.nlm.nih.gov/nuccore/2440446687 | ||
| # biosample here: https://www.ncbi.nlm.nih.gov/biosample?term=SAMN33060589 | ||
| # one of the sample included in initial pango-designation here: https://github.com/cov-lineages/pango-designation/issues/1723 | ||
| RUN datasets download virus genome accession OQ381818.1 --filename OQ381818.1.zip && \ | ||
| unzip OQ381818.1.zip && rm OQ381818.1.zip && \ | ||
| mv -v ncbi_dataset/data/genomic.fna OQ381818.1.genomic.fna && \ | ||
| rm -vr ncbi_dataset/ README.md && \ | ||
| pangolin OQ381818.1.genomic.fna -o OQ381818.1-usher && \ | ||
| column -t -s, OQ381818.1-usher/lineage_report.csv | ||
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| # testing another XBB.1.16, trying to test scorpio functionality. Want pangolin to NOT assign lineage based on pango hash match. | ||
| # this test runs as expected, uses scorpio to check for constellation of mutations, then assign using PUSHER placement | ||
| RUN datasets download virus genome accession OR177999.1 --filename OR177999.1.zip && \ | ||
| unzip OR177999.1.zip && rm OR177999.1.zip && \ | ||
| mv -v ncbi_dataset/data/genomic.fna OR177999.1.genomic.fna && \ | ||
| rm -vr ncbi_dataset/ README.md && \ | ||
| pangolin OR177999.1.genomic.fna -o OR177999.1-usher && \ | ||
| column -t -s, OR177999.1-usher/lineage_report.csv | ||
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| ## test for BA.2.86 | ||
| # virus identified in MI: https://www.ncbi.nlm.nih.gov/nuccore/OR461132.1 | ||
| RUN datasets download virus genome accession OR461132.1 --filename OR461132.1.zip && \ | ||
| unzip OR461132.1.zip && rm OR461132.1.zip && \ | ||
| mv -v ncbi_dataset/data/genomic.fna OR461132.1.genomic.fna && \ | ||
| rm -vr ncbi_dataset/ README.md && \ | ||
| pangolin OR461132.1.genomic.fna -o OR461132.1-usher && \ | ||
| column -t -s, OR461132.1-usher/lineage_report.csv | ||
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| ## test for JN.2 (BA.2.86 sublineage) JN.2 is an alias of B.1.1.529.2.86.1.2 | ||
| # NY CDC Quest sample: https://www.ncbi.nlm.nih.gov/nuccore/OR598183 | ||
| RUN datasets download virus genome accession OR598183.1 --filename OR598183.1.zip && \ | ||
| unzip OR598183.1.zip && rm OR598183.1.zip && \ | ||
| mv -v ncbi_dataset/data/genomic.fna OR598183.1.genomic.fna && \ | ||
| rm -vr ncbi_dataset/ README.md && \ | ||
| pangolin OR598183.1.genomic.fna -o OR598183.1-usher && \ | ||
| column -t -s, OR598183.1-usher/lineage_report.csv | ||
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| ## test for JQ.1 (BA.2.86.3 sublineage); JQ.1 is an alias of B.1.1.529.2.86.3.1 | ||
| # THANK YOU ERIN AND UPHL!! https://www.ncbi.nlm.nih.gov/nuccore/OR716684 | ||
| # this test is important due to the fact that this lineage was included in the UShER tree, despite being designated after the pangolin-designation 1.23 release | ||
| # it previously caused and error/bug in pangolin, but now is fixed | ||
| RUN datasets download virus genome accession OR716684.1 --filename OR716684.1.zip && \ | ||
| unzip OR716684.1.zip && rm OR716684.1.zip && \ | ||
| mv -v ncbi_dataset/data/genomic.fna OR716684.1.genomic.fna && \ | ||
| rm -vr ncbi_dataset/ README.md && \ | ||
| pangolin OR716684.1.genomic.fna -o OR716684.1-usher && \ | ||
| column -t -s, OR716684.1-usher/lineage_report.csv | ||
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| ## test for JN.1.22 (BA.2.86.x sublineage; full unaliased lineage is B.1.1.529.2.86.1.1.22) | ||
| # see here for commit where it was designated https://github.com/cov-lineages/pango-designation/commit/a90c8e31c154621ed86c985debfea09e17541cda | ||
| # Here's the genome on NCBI, which was used to designate JN.1.22 lineage | ||
| RUN datasets download virus genome accession PP189069.1 --filename PP189069.1.zip && \ | ||
| unzip PP189069.1.zip && rm PP189069.1.zip && \ | ||
| mv -v ncbi_dataset/data/genomic.fna PP189069.1.genomic.fna && \ | ||
| rm -vr ncbi_dataset/ README.md && \ | ||
| pangolin PP189069.1.genomic.fna -o PP189069.1-usher && \ | ||
| column -t -s, PP189069.1-usher/lineage_report.csv |
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