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update freyja to version 1.5.1 (#991)
* update freyja to version 1.5.1 * added pyarrow * updated version
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| FROM mambaorg/micromamba:1.5.6 as app | ||
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| # Version arguments | ||
| # ARG variables only persist during build time | ||
| ARG FREYJA_SOFTWARE_VERSION="1.5.1" | ||
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| # build and run as root users since micromamba image has 'mambauser' set as the $USER | ||
| USER root | ||
| # set workdir to default for building; set to /data at the end | ||
| WORKDIR / | ||
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| LABEL base.image="mambaorg/micromamba:1.5.6" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="Freyja" | ||
| LABEL software.version=${FREYJA_SOFTWARE_VERSION} | ||
| LABEL description="Freyja is a tool to recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference)" | ||
| LABEL website="https://github.com/andersen-lab/Freyja" | ||
| LABEL license="https://github.com/andersen-lab/Freyja/blob/main/LICENSE" | ||
| LABEL maintainer="Kevin Libuit" | ||
| LABEL maintainer.email="[email protected]" | ||
| LABEL maintainer2="Curtis Kapsak" | ||
| LABEL maintainer2.email="[email protected]" | ||
| LABEL maintainer3="Erin Young" | ||
| LABEL maintainer3.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 \ | ||
| procps && \ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
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| # Create Freyja conda environment called freyja-env from bioconda recipe | ||
| # clean up conda garbage | ||
| RUN micromamba create -n freyja-env -c conda-forge -c bioconda -c defaults freyja=${FREYJA_SOFTWARE_VERSION} && \ | ||
| micromamba clean -a -y | ||
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| # set the environment, put new conda env in PATH by default | ||
| ENV PATH="/opt/conda/envs/freyja-env/bin:/opt/conda/envs/env/bin:${PATH}" \ | ||
| LC_ALL=C.UTF-8 | ||
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| RUN pip install pyarrow | ||
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| # update barcodes | ||
| # NOTE: this will download the latest version of the `freyja/data/usher_barcodes.csv` file from GitHub | ||
| RUN freyja update | ||
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| # set working directory to /data | ||
| WORKDIR /data | ||
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| # default command is to pull up help options | ||
| CMD [ "freyja", "--help" ] | ||
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| # new base for testing | ||
| FROM app as test | ||
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| RUN freyja --help && freyja --version | ||
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| # Grab test data from Freyja version 1.3.4 | ||
| RUN wget -O /data/Freyja_WWSC2.bam https://github.com/StaPH-B/docker-builds/blob/master/freyja/1.3.4/tests/Freyja_WWSC2.bam?raw=true && \ | ||
| wget -P /data https://raw.githubusercontent.com/StaPH-B/docker-builds/master/freyja/1.3.4/tests/Freyja_depths.tsv && \ | ||
| wget -P /data https://raw.githubusercontent.com/StaPH-B/docker-builds/master/freyja/1.3.4/tests/Freyja_variants.tsv && \ | ||
| wget -P /data https://raw.githubusercontent.com/StaPH-B/docker-builds/master/freyja/1.3.4/tests/nCoV-2019.reference.fasta | ||
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| # Run Freyja | ||
| RUN freyja variants /data/Freyja_WWSC2.bam --variants /data/test_variants.tsv --depths /data/test_depths.tsv --ref /data/nCoV-2019.reference.fasta && \ | ||
| freyja demix /data/test_variants.tsv /data/test_depths.tsv --output /data/test_demix.tsv | ||
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| # Check validity of outputs | ||
| RUN head /data/test_variants.tsv && \ | ||
| head /data/test_depths.tsv && \ | ||
| head /data/test_demix.tsv && \ | ||
| grep "Omicron" /data/test_demix.tsv | ||
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| # print barcode version and freyja version | ||
| RUN freyja demix --version |
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| # freyja container | ||
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| Main tool & documentation: [freyja](https://github.com/andersen-lab/Freyja) | ||
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| Freyja is a tool to recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference). The method uses lineage-determining mutational "barcodes" derived from the UShER global phylogenetic tree as a basis set to solve the constrained (unit sum, non-negative) de-mixing problem. | ||
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| ## freyja barcodes | ||
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| This docker image was built on **2024-06-25** and the command `freyja update` is run as part of the build to retrieve the most up-to-date barcode file `freyja/data/usher_barcodes.csv` file from Freyja's GitHub repo. The barcode version included in this docker image is **`06_25_2024-01-22`** as reported by `freyja demix --version` | ||
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| This image is rebuilt every day on Dockerhub and Quay.io with the tag ${freyja version}-${freyja database version}-${data image was deployed}. | ||
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| ## Example Usage | ||
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| ```bash | ||
| # run freyja variants to call variants from an aligned SC2 bam file | ||
| freyja variants [bamfile] --variants [variant outfile name] --depths [depths outfile name] --ref [reference.fa] | ||
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| # run freyja demix to identify lineages based on called variants | ||
| freyja demix [variants-file] [depth-file] --output [output-file] | ||
| ``` | ||
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| Warning: `freyja update` does not work under all conditions. You may need to specify an output directory (`freyja update --outdir /path/to/outdir`) for which your user has write privileges, such as a mounted volume. |