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| ARG ARTIC_VER=1.5.8 | ||
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| FROM mambaorg/micromamba:1.5.8 AS app | ||
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| ARG ARTIC_VER | ||
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| LABEL base.image="mambaorg/micromamba:1.5.8" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="artic" | ||
| LABEL software.version="${ARTIC_VER}" | ||
| LABEL description="A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore" | ||
| LABEL website="https://github.com/artic-network/fieldbioinformatics" | ||
| LABEL license="https://github.com/artic-network/fieldbioinformatics/blob/master/LICENSE" | ||
| LABEL sop="https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html" | ||
| LABEL maintainer="Erin Young" | ||
| LABEL maintainer.email="[email protected]" | ||
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| USER root | ||
| WORKDIR / | ||
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| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| wget \ | ||
| ca-certificates \ | ||
| procps \ | ||
| gcc \ | ||
| make \ | ||
| pkg-config \ | ||
| zlib1g-dev \ | ||
| libbz2-dev \ | ||
| liblzma-dev \ | ||
| libcurl4-gnutls-dev \ | ||
| libssl-dev \ | ||
| python3-dev \ | ||
| python3-pip \ | ||
| python-is-python3 && \ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
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| RUN micromamba create -n artic -y -c conda-forge -c bioconda -c defaults \ | ||
| artic=${ARTIC_VER} && \ | ||
| micromamba clean -a -f -y && \ | ||
| mkdir /data | ||
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| ENV PATH="${PATH}:/opt/conda/envs/artic/bin/" \ | ||
| CONDA_PREFIX="/opt/conda/envs/artic/" \ | ||
| LC_ALL=C.UTF-8 | ||
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| RUN artic_get_models | ||
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| CMD artic --help | ||
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| WORKDIR /data | ||
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| ##### ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ##### | ||
| ##### Step 2. Set up the testing stage. ##### | ||
| ##### The docker image is built to the 'test' stage before merging, but ##### | ||
| ##### the test stage (or any stage after 'app') will be lost. ##### | ||
| ##### ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ##### | ||
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| # A second FROM insruction creates a new stage | ||
| # new base for testing | ||
| FROM app AS test | ||
| ARG ARTIC_VER | ||
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| # print help and version info; check dependencies (not all software has these options available) | ||
| # Mostly this ensures the tool of choice is in path and is executable | ||
| RUN artic --help && \ | ||
| artic --version | ||
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| WORKDIR / | ||
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| # test that came with artic | ||
| RUN wget -q https://github.com/artic-network/fieldbioinformatics/archive/refs/tags/v${ARTIC_VER}.tar.gz && \ | ||
| tar -vxf v${ARTIC_VER}.tar.gz && \ | ||
| cd /fieldbioinformatics-${ARTIC_VER} && ls && \ | ||
| bash ./test-runner.sh clair3 | ||
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| WORKDIR /test | ||
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| # using on "real" data (sample files were not sequenced with version 5.3.2 primers) | ||
| # filtering fastq files | ||
| RUN wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR224/050/SRR22452250/SRR22452250_1.fastq.gz && \ | ||
| artic guppyplex --min-length 400 --max-length 700 --directory . --prefix SRR22452250_1.fastq.gz --output SRR22452250_1_filtered.fastq.gz | ||
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| # running artic minion with user-provided bed and reference | ||
| RUN wget -q https://raw.githubusercontent.com/artic-network/primer-schemes/master/nCoV-2019/V5.3.2/SARS-CoV-2.primer.bed && \ | ||
| wget -q https://raw.githubusercontent.com/artic-network/primer-schemes/master/nCoV-2019/V5.3.2/SARS-CoV-2.reference.fasta && \ | ||
| artic minion --normalise 200 --threads 4 --model ont --read-file SRR22452250_1_filtered.fastq.gz --bed SARS-CoV-2.primer.bed --ref SARS-CoV-2.reference.fasta test1 && \ | ||
| ls test1* | ||
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| # running artic as it pulls schemes from github | ||
| RUN artic minion --normalise 200 --threads 4 --model ont --read-file SRR22452250_1_filtered.fastq.gz --scheme-name sars-cov-2 --scheme-version V5.3.2 test2 && \ | ||
| ls test2* | ||
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| RUN echo "included models" && \ | ||
| ls ${CONDA_PREFIX}/bin/models |
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| # artic fieldbioinformatics container | ||
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| Main tool : [artic](https://github.com/artic-network/fieldbioinformatics) | ||
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| Full documentation: [https://github.com/artic-network/fieldbioinformatics](https://github.com/artic-network/fieldbioinformatics) | ||
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| There is also a very useful SOP: [https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html](https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html) | ||
| And additional documentation: [https://artic.readthedocs.io/en/latest/](https://artic.readthedocs.io/en/latest/) | ||
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| > A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore. | ||
| WARNING : This container does not contain the primer schemes found at [https://github.com/artic-network/primer-schemes](https://github.com/artic-network/primer-schemes). Those will have to be downloaded and mounted separately. There are now commands to download the use the primers at runtime. | ||
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| This image DOES contain the medaka models downloaded with `artic_get_models` | ||
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| ## Example Usage with the artic primers | ||
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| ```bash | ||
| # filtering reads | ||
| artic guppyplex --min-length 400 --max-length 700 --directory . --prefix SRR22452250_1.fastq.gz --output SRR22452250_1_filtered.fastq.gz | ||
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| # downloading medaka models for clair3 | ||
| artic_get_models | ||
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| # running the artic minion workflow | ||
| # the result files will all start with test* | ||
| artic minion --normalise 200 --medaka-model ont --threads 4 --read-file sample.fastq.gz --scheme-directory primer-schemes --scheme-version 5.3.2 nCoV-2019 test | ||
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| # running the artic minion workflow with user-provided primer bedfiles and references | ||
| artic minion --normalise 200 --threads 4 --model ont --read-file sample.fastq.gz --scheme-name sars-cov-2 --scheme-version V5.3.2 name | ||
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| ``` | ||
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| In general, any primer scheme can be used as long as it meets [artic's requirements](https://github.com/artic-network/primer-schemes). | ||
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| ## Medaka models | ||
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| Artic uses [Clair3](https://github.com/HKU-BAL/Clair3), which uses medaka models. Medaka updates frequently, and artic can throw errors when corresponding ONT models are not found. | ||
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| These are the medaka models in this image: | ||
| ``` | ||
| # included models at /opt/conda/envs/artic/bin/models | ||
| hifi | ||
| hifi_revio | ||
| hifi_sequel2 | ||
| ilmn | ||
| ont | ||
| ont_guppy5 | ||
| r1041_e82_260bps_fast_g632 | ||
| r1041_e82_260bps_hac_g632 | ||
| r1041_e82_260bps_hac_v400 | ||
| r1041_e82_260bps_hac_v410 | ||
| r1041_e82_260bps_sup_g632 | ||
| r1041_e82_260bps_sup_v400 | ||
| r1041_e82_260bps_sup_v410 | ||
| r1041_e82_400bps_fast_g632 | ||
| r1041_e82_400bps_hac_g615 | ||
| r1041_e82_400bps_hac_g632 | ||
| r1041_e82_400bps_hac_v400 | ||
| r1041_e82_400bps_hac_v410 | ||
| r1041_e82_400bps_hac_v420 | ||
| r1041_e82_400bps_hac_v430 | ||
| r1041_e82_400bps_hac_v500 | ||
| r1041_e82_400bps_sup_g615 | ||
| r1041_e82_400bps_sup_v400 | ||
| r1041_e82_400bps_sup_v410 | ||
| r1041_e82_400bps_sup_v420 | ||
| r1041_e82_400bps_sup_v430 | ||
| r1041_e82_400bps_sup_v500 | ||
| r104_e81_hac_g5015 | ||
| r104_e81_sup_g5015 | ||
| r941_prom_hac_g360+g422 | ||
| r941_prom_sup_g5014 | ||
| ``` |