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* add genoflu * add readme * add to license * add --force-pkgs-dirs * krakentools add * update readmes * silence warnings about AS casing; fix typo * added comment in dockerfile & added additional dependencies and versions to readme for krakentools * pinning biopython and pandas versions and removing unnecessary jq and gawk * fixed version of python installed listed in krakentools readme * add tbprofiler 6.4.0 * update readme * add list_db * exec format, capitalize AS * update versions * pinning delly version due to conflict resolution with usher 0.6.3 which is required by tb-profiler * added delly to list of deps for tb-profiler. Plus link to GH issue describing troubles w delly * add 6.4.1 * update readme * correct versions of a few dependencies in tbprofiler readme * Update Dockerfile * Update README.md --------- Co-authored-by: Curtis Kapsak <[email protected]>
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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="6.4.1" | ||
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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 2024-10-31 | ||
| ARG TBDB_COMMIT="2c92475219416a449e89782f2b768149d26f7979" | ||
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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 -f && micromamba list | ||
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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 | ||
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| # https://github.com/jodyphelan/tbdb | ||
| RUN tb-profiler update_tbdb --commit ${TBDB_COMMIT} && \ | ||
| tb-profiler list_db | ||
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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 `2c92475`. This is from the GitHub repository https://github.com/jodyphelan/tbdb. This can be confirmed in the json file: `/opt/conda/share/tbprofiler/tbdb.variables.json`: | ||
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| ```bash | ||
| $ grep 'commit' /opt/conda/share/tbprofiler/tbdb.variables.json | ||
| {"db-schema-version": "1.0.0", "snpEff_db": "Mycobacterium_tuberculosis_h37rv", "drugs": ["rifampicin", "isoniazid", "ethambutol", "pyrazinamide", "moxifloxacin", "levofloxacin", "bedaquiline", "delamanid", "pretomanid", "linezolid", "streptomycin", "amikacin", "kanamycin", "capreomycin", "clofazimine", "ethionamide", "para-aminosalicylic_acid", "cycloserine"], "tb-profiler-version": ">=6.0.0,<7.0.0", "version": {"name": "tbdb", "commit": "2c92475", "Merge": "8918884 2a51937", "Author": "Jody Phelan <[email protected]>", "Date": "Mon Oct 7 17:06:42 2024 +0100", "db-schema-version": "1.0.0"}, "amplicon": false, "files": {"ref": "tbdb.fasta", "gff": "tbdb.gff", "bed": "tbdb.bed", "json_db": "tbdb.dr.json", "variables": "tbdb.variables.json", "spoligotype_spacers": "tbdb.spoligotype_spacers.txt", "spoligotype_annotations": "tbdb.spoligotype_list.csv", "bedmask": "tbdb.mask.bed", "barcode": "tbdb.barcode.bed", "rules": "tbdb.rules.txt"}} | ||
| ``` | ||
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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 2c92475 Jody Phelan <[email protected]> Mon Oct 7 17:06:42 2024 +0100 /opt/conda/share/tbprofiler/tbdb | ||
| ``` | ||
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| ## Additional included tools/dependencies | ||
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| - bedtools 2.31.1 | ||
| - gatk4 4.6.1.0 | ||
| - kmc 3.2.4 | ||
| - pathogen-profiler 4.5.1 | ||
| - perl 5.32.1 | ||
| - python 3.12.7 | ||
| - trimmomatic 0.39 | ||
| - bwa 0.7.18 | ||
| - minimap2 2.28 | ||
| - samtools 1.21 | ||
| - bcftools 1.21 | ||
| - freebayes 1.3.6 | ||
| - tqdm 4.67.0 | ||
| - parallel 20240922 | ||
| - samclip 0.4.0 | ||
| - snpeff 5.2 | ||
| - delly 1.2.6 (the more recent version 1.3.1 did not allow for the conda environment to resolve; TBProfiler has specifically pinned v1.2.6. More info here: https://github.com/jodyphelan/TBProfiler/issues/393#issuecomment-2452076859) | ||
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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 | ||
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| 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/) |