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Merge pull request StaPH-B#670 from StaPH-B/cjk-pangolin-update
add pangolin 4.3 & pdata 1.20
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| FROM mambaorg/micromamba:1.4.3 as app | ||
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| # build and run as root users since micromamba image has 'mambauser' set as the $USER | ||
| USER root | ||
| # set workdir to default for building; set to /data at the end | ||
| WORKDIR / | ||
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| # ARG variables only persist during build time | ||
| # had to include the v for some of these due to GitHub tags. | ||
| # using pangolin-data github tag, NOT what is in the GH release title "v1.2.133" | ||
| ARG PANGOLIN_VER="v4.3" | ||
| ARG PANGOLIN_DATA_VER="v1.20" | ||
| ARG SCORPIO_VER="v0.3.17" | ||
| ARG CONSTELLATIONS_VER="v0.1.10" | ||
| ARG USHER_VER="0.6.2" | ||
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| # metadata labels | ||
| LABEL base.image="mambaorg/micromamba:1.4.3" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="pangolin" | ||
| LABEL software.version=${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 | ||
| # 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 && \ | ||
| 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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| WORKDIR /data | ||
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| # hardcode pangolin executable into the PATH variable | ||
| ENV PATH="${PATH}:/opt/conda/envs/pangolin/bin/" | ||
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| # default command is to pull up help options for virulencefinder; 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 --analysis-mode usher -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 --analysis-mode usher -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 --analysis-mode usher -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 --analysis-mode usher -o OQ381818.1-usher && \ | ||
| column -t -s, OQ381818.1-usher/lineage_report.csv |
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| # pangolin docker image | ||
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| Main tool : [pangolin](https://github.com/cov-lineages/pangolin) | ||
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| Full documentation: [https://cov-lineages.org/resources/pangolin.html](https://cov-lineages.org/resources/pangolin.html) | ||
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| Phylogenetic Assignment of Named Global Outbreak LINeages | ||
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| Additional tools: | ||
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| - [pangolin-data](https://github.com/cov-lineages/pangolin-data) 1.20 | ||
| - [pangolin-assignment](https://github.com/cov-lineages/pangolin-assignment) 1.20 | ||
| - [minimap2](https://github.com/lh3/minimap2) 2.26-r1175 | ||
| - [usher](https://github.com/yatisht/usher) 0.6.2 | ||
| - [faToVcf](https://github.com/yatisht/usher) 426 | ||
| - [scorpio](https://github.com/cov-lineages/scorpio) 0.3.17 | ||
| - [constellations](https://github.com/cov-lineages/constellations) 0.1.10 | ||
| - [gofasta](https://github.com/virus-evolution/gofasta) 1.2.0 | ||
| - [mafft](https://mafft.cbrc.jp/alignment/software/) 7.520 | ||
| - python 3.8.15 | ||
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| ## pangoLEARN deprecation | ||
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| As of pangolin version 4.3, pangoLEARN mode has been deprecated. [More info can be found here on the v4.3 release page.](https://github.com/cov-lineages/pangolin/releases/tag/v4.3) | ||
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| > If `--analysis-mode fast` or `--analysis-mode pangolearn` is given, pangolin v4.3 will print out a warning and use UShER mode instead, unless `--datadir` is also given specifying a directory with pangoLEARN model files. The next release of pangolin-data (v1.20) will no longer include the model files which have not been updated since v1.18. | ||
| This docker image contains `pangolin-data` v1.20. The pangoLEARN model has not been updated since pangolin-data version 1.18. Only the the underlying UShER tree/protobuf file will be maintained for the forseeable future. | ||
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| **Please use the UShER mode of pangolin if you want to stay up-to-date with the most recent lineages.** [See pangolin-data release notes here for more details](https://github.com/cov-lineages/pangolin-data/releases/tag/v1.20) | ||
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| ## Example Usage | ||
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| ```bash | ||
| # run Pangolin in the default mode (usher). Can optionally supply --analysis-mode usher | ||
| $ pangolin /pangolin/pangolin/test/test_seqs.fasta -o /data/test_seqs-output-pusher | ||
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| # view the output CSV | ||
| $ column -t -s, /data/test_seqs-output-pusher/lineage_report.csv | ||
| taxon lineage conflict ambiguity_score scorpio_call scorpio_support scorpio_conflict scorpio_notes version pangolin_version scorpio_version constellation_version is_designated qc_status qc_notes note | ||
| India seq B.1.617.1 0.0 B.1.617.1-like 1.0 0.0 scorpio call: Alt alleles 11; Ref alleles 0; Amb alleles 0; Oth alleles 0 PUSHER-v1.16 4.1.3 0.3.17 v0.1.10 False pass Ambiguous_content:0.02 Usher placements: B.1.617.1(1/1) | ||
| b117 B.1.1.7 0.0 Alpha (B.1.1.7-like) 0.91 0.04 scorpio call: Alt alleles 21; Ref alleles 1; Amb alleles 1; Oth alleles 0 PUSHER-v1.16 4.1.3 0.3.17 v0.1.10 False pass Ambiguous_content:0.02 Usher placements: B.1.1.7(2/2) | ||
| outgroup_A A 0.0 PUSHER-v1.16 4.1.3 0.3.17 v0.1.10 False pass Ambiguous_content:0.02 Usher placements: A(1/1) | ||
| issue_57_torsten_seq Unassigned PUSHER-v1.16 4.1.3 0.3.17 v0.1.10 False fail failed to map | ||
| This_seq_has_6000_Ns_in_18000_bases Unassigned PUSHER-v1.16 4.1.3 0.3.17 v0.1.10 False fail failed to map | ||
| This_seq_has_no_seq Unassigned PUSHER-v1.16 4.1.3 0.3.17 v0.1.10 False fail failed to map | ||
| This_seq_is_too_short Unassigned PUSHER-v1.16 4.1.3 0.3.17 v0.1.10 False fail Ambiguous_content:0.9 | ||
| This_seq_has_lots_of_Ns Unassigned PUSHER-v1.16 4.1.3 0.3.17 v0.1.10 False fail Ambiguous_content:0.98 | ||
| This_seq_is_literally_just_N Unassigned PUSHER-v1.16 4.1.3 0.3.17 v0.1.10 False fail failed to map | ||
| Japan_seq B 0.0 PANGO-v1.16 4.1.3 0.3.17 v0.1.10 True pass Ambiguous_content:0.02 Assigned from designation hash. | ||
| USA_seq B.1.314 0.0 PANGO-v1.16 4.1.3 0.3.17 v0.1.10 True pass Ambiguous_content:0.02 Assigned from designation hash. | ||
| Unassigned_omicron_seq BA.1 0.0 Probable Omicron (BA.1-like) 0.71 0.08 scorpio call: Alt alleles 42; Ref alleles 5; Amb alleles 9; Oth alleles 3 PUSHER-v1.16 4.1.3 0.3.17 v0.1.10 False pass Ambiguous_content:0.03 Usher placements: BA.1(1/1) | ||
| ``` |