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Merge pull request #974 from sage-wright/master
add tbprofiler version 6.2.1
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| FROM mambaorg/micromamba:1.5.8 as app | ||
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| USER root | ||
| WORKDIR / | ||
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| ARG TBPROFILER_VER="6.2.1" | ||
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| # this version is the shortened commit hash on the `master` branch here https://github.com/jodyphelan/tbdb/ | ||
| # commits are found on https://github.com/jodyphelan/tbdb/commits/master | ||
| # this was the latest commit as of 2024-05-10 | ||
| ARG TBDB_COMMIT="97b5876a1a9d2f06e8bb6076ed88baf481ef5fe5" | ||
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| # LABEL instructions tag the image with metadata that might be important to the user | ||
| LABEL base.image="micromamba:1.5.8" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="tbprofiler" | ||
| LABEL software.version="${TBPROFILER_VER}" | ||
| LABEL description="The pipeline aligns reads to the H37Rv reference using bowtie2, BWA or minimap2 and then calls variants using bcftools. These variants are then compared to a drug-resistance database." | ||
| LABEL website="https://github.com/jodyphelan/TBProfiler/" | ||
| LABEL license="https://github.com/jodyphelan/TBProfiler/blob/master/LICENSE" | ||
| LABEL maintainer="John Arnn" | ||
| LABEL maintainer.email="[email protected]" | ||
| LABEL maintainer2="Curtis Kapsak" | ||
| LABEL maintainer2.email="[email protected]" | ||
| LABEL maintainer3="Sage Wright" | ||
| LABEL maintainer3.email="[email protected]" | ||
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| # Install dependencies via apt-get; cleanup apt garbage | ||
| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| wget \ | ||
| ca-certificates \ | ||
| procps && \ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
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| # install tb-profiler via bioconda; install into 'base' conda env | ||
| RUN micromamba install --yes --name base --channel conda-forge --channel bioconda \ | ||
| tb-profiler=${TBPROFILER_VER} && \ | ||
| micromamba clean --all --yes | ||
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| # hardcode 'base' env bin into PATH, so conda env does not have to be "activated" at run time | ||
| ENV PATH="/opt/conda/bin:${PATH}" | ||
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| # Version of database can be confirmed at /opt/conda/share/tbprofiler/tbdb.version.json | ||
| # can also run 'tb-profiler list_db' to find the same version info | ||
| # In 5.0.1 updating_tbdb does not work with tb-profiler update_tbdb --commit ${TBDB_VER} | ||
| # ^^ this was resolved in 6.2.1 | ||
| #RUN tb-profiler update_tbdb -h && whatever | ||
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| # https://github.com/jodyphelan/tbdb | ||
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| RUN tb-profiler update_tbdb --commit ${TBDB_COMMIT} | ||
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| WORKDIR /data | ||
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| # Added command to bring help menu up upon running container. | ||
| CMD tb-profiler | ||
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| # test stage | ||
| FROM app as test | ||
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| # checking if tool is in PATH | ||
| RUN tb-profiler && tb-profiler version | ||
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| WORKDIR /tests | ||
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| # download some TB FASTQs and run through tb-profiler | ||
| RUN wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR166/009/ERR1664619/ERR1664619_1.fastq.gz && \ | ||
| wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR166/009/ERR1664619/ERR1664619_2.fastq.gz && \ | ||
| tb-profiler profile -1 ERR1664619_1.fastq.gz -2 ERR1664619_2.fastq.gz -t 2 -p ERR1664619 --txt |
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| # TBProfiler Container | ||
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| Main tool: [TBProfiler](https://github.com/jodyphelan/TBProfiler) | ||
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| The pipeline aligns reads to the H37Rv reference using bowtie2, BWA or minimap2 and then calls variants using bcftools. These variants are then compared to a drug-resistance database. It also predicts the number of reads supporting drug resistance variants as an insight into hetero-resistance. | ||
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| ## Database | ||
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| This tool relies on a database to run. The version (AKA git commit hash) of the database that is included in the docker image is `97b5876`. This is from the GitHub repository https://github.com/jodyphelan/tbdb. This can be confirmed in the json file: `/opt/conda/share/tbprofiler/tbdb.version.json`: | ||
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| ```bash | ||
| $ grep 'commit' /opt/conda/share/tbprofiler/tbdb.version.json | ||
| {"name": "tbdb", "commit": "5f3c51e", "Merge": "b1a2549 abddb8e", "Author": "Jody Phelan <[email protected]>", "Date": "Thu Jan 19 10:47:32 2023 +0000"} | ||
| ``` | ||
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| Additionally you can run the command `tb-profiler list_db` to list the same information | ||
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| ```bash | ||
| $ tb-profiler list_db | ||
| tbdb 97b5876 Jody Phelan <[email protected]> Wed May 8 13:53:15 2024 +0100 /opt/conda/share/tbprofiler/tbdb | ||
| ``` | ||
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| ## Additional included tools/dependencies | ||
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| - bedtools 2.31.1 | ||
| - gatk4 4.5.0.0 | ||
| - kmc 3.2.4 | ||
| - pathogen-profiler 4.2.0 | ||
| - perl 5.32.1 | ||
| - python 3.10.14 | ||
| - trimmomatic 0.39 | ||
| - bwa 0.7.18 | ||
| - minimap2 2.28 | ||
| - samtools 1.20 | ||
| - bcftools 1.20 | ||
| - freebayes 1.3.6 | ||
| - tqdm 4.66.4 | ||
| - parallel 20240522 | ||
| - samclip 0.4.0 | ||
| - snpeff 5.2 | ||
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| ## Example Usage | ||
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| Run whole pipeline on Illumina paired-end reads: | ||
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| ```bash | ||
| tb-profiler profile -1 ERR1664619_1.fastq.gz -2 ERR1664619_2.fastq.gz -t 4 -p ERR1664619 --txt | ||
| ``` | ||
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| Make alternative database: | ||
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| ```bash | ||
| tb-profiler create_db --prefix <new_library_name> | ||
| tb-profiler load_library --prefix <new_library_name> | ||
| ``` | ||
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| ## Updates | ||
| Release 5.0.1 implemented sqlite3 database locking with https://py-filelock.readthedocs.io/en/latest/index.html. This should fix issues using it over network filing systems (NFS). For more information, official documentation can be found [here.](https://jodyphelan.gitbook.io/tb-profiler/) |