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adding longshot version 0.4.5 #721
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| Original file line number | Diff line number | Diff line change |
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| FROM mambaorg/micromamba:1.4.9 as app | ||
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| # List all software versions are ARGs near the top of the dockerfile | ||
| # 'ARG' sets environment variables during the build stage | ||
| # 'ARG' variables are ONLY available during image build, they do not persist in the final image | ||
| ARG LONGSHOT_VERSION="0.4.5" | ||
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| # build and run as root users since micromamba image has 'mambauser' set as the $USER | ||
| USER root | ||
| # set workdir to default for building; set to /data at the end | ||
| WORKDIR / | ||
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| # 'LABEL' instructions tag the image with metadata that might be important to the user | ||
| LABEL base.image="mambaorg/micromamba:1.4.9" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="longshot" | ||
| LABEL software.version="${LONGSHOT_VERSION}" | ||
| LABEL description="A variant calling tool for noisy reads" | ||
| LABEL website="https://github.com/pjedge/longshot" | ||
| LABEL license="https://github.com/pjedge/longshot/blob/master/LICENSE" | ||
| LABEL maintainer="Erin Young" | ||
| LABEL maintainer.email="[email protected]" | ||
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| # Example apt-get command for commonly-missing dependencies | ||
| 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 your desired software into the base conda/micromamba environment, pinning the version | ||
| # clean up conda garbage | ||
| # make /data to use as a working directory | ||
| RUN micromamba install --name base -c conda-forge -c bioconda -c defaults longshot=${LONGSHOT_VERSION} && \ | ||
| micromamba clean -a -y && \ | ||
| mkdir /data | ||
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| # 'ENV' instructions set environment variables that persist from the build into the resulting image | ||
| # set the environment, add base conda/micromamba bin directory into path | ||
| # set locale settings to UTF-8 | ||
| ENV PATH="/opt/conda/bin/:${PATH}" \ | ||
| LC_ALL=C.UTF-8 | ||
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| # 'CMD' instructions set a default command when the container is run. This is typically 'tool --help.' | ||
| CMD longshot --help | ||
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| # set final working directory to /data | ||
| 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 | ||
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| # so that conda/micromamba env is active when running below commands | ||
| ENV ENV_NAME="base" | ||
| ARG MAMBA_DOCKERFILE_ACTIVATE=1 | ||
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| # set working directory so that all test inputs & outputs are kept in /test | ||
| WORKDIR /test | ||
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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 longshot --help && \ | ||
| longshot --version | ||
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| RUN wget -q https://raw.githubusercontent.com/pjedge/longshot/master/example_data/genome.fa && \ | ||
| wget -q https://raw.githubusercontent.com/pjedge/longshot/master/example_data/genome.fa.fai && \ | ||
| wget -q https://raw.githubusercontent.com/pjedge/longshot/master/example_data/ground_truth_variants.vcf && \ | ||
| wget -q https://raw.githubusercontent.com/pjedge/longshot/master/example_data/pacbio_reads_30x.bam && \ | ||
| wget -q https://raw.githubusercontent.com/pjedge/longshot/master/example_data/pacbio_reads_30x.bam.bai && \ | ||
| longshot --bam pacbio_reads_30x.bam --ref genome.fa --out longshot_output.vcf && \ | ||
| head *vcf |
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| Original file line number | Diff line number | Diff line change |
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| # longshot container | ||
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| Main tool : [longshot](https://github.com/pjedge/longshot) | ||
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| Code repository: https://github.com/pjedge/longshot | ||
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| Basic information on how to use this tool: | ||
| - executable: longshot | ||
| - help: <--help> | ||
| - version: <--version> | ||
| - description: Longshot is a variant calling tool for diploid genomes using long error-prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT). | ||
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| Additional information: | ||
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| Longshot takes as input an aligned BAM/CRAM file and outputs a phased VCF file with variants and haplotype information. It can also genotype and phase input VCF files. It can output haplotype-separated BAM files that can be used for downstream analysis. Currently, it only calls single nucleotide variants (SNVs), but it can genotype indels if they are given in an input VCF. | ||
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| Full documentation: [https://github.com/artic-network/fieldbioinformatics](https://github.com/artic-network/fieldbioinformatics) | ||
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| ## Example Usage | ||
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| ```bash | ||
| longshot --bam example_data/pacbio_reads_30x.bam --ref example_data/genome.fa --out example_data/longshot_output.vcf | ||
| ``` | ||
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I modified Read Me to comply with new templates and trigger checks.