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* added version 2.31.1 * readjusted labels and tests
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| ARG BEDTOOLS_VER="2.31.1" | ||
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| ### builder stage for compiling bedtools code ### | ||
| FROM ubuntu:jammy as builder | ||
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| # re-instantiate variable so we can use it in builder stage | ||
| ARG BEDTOOLS_VER | ||
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| # install deps via apt-get, these are mainly for compiling bedtools code and for running tests. some are for downloading files (wget, ca-certificates) | ||
| # last command is to point 'python' cmd to `python3` so that bedtools test scripts work. There are bash scripts that call 'python' | ||
| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| build-essential \ | ||
| zlib1g-dev \ | ||
| libghc-bzlib-dev \ | ||
| liblzma-dev \ | ||
| wget \ | ||
| ca-certificates \ | ||
| python3 && \ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* && \ | ||
| update-alternatives --install /usr/bin/python python /usr/bin/python3 10 | ||
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| # python3 required when compiling via `make` command for creating old CLI executables | ||
| # dependencies listed here (albeit for v2.30.0, still should be identical): https://packages.ubuntu.com/jammy/bedtools | ||
| # requires libghc-bzlib-dev, build-essential, zlib1g-dev, and a few others | ||
| # 'make install' should place binary executable files in /usr/local/bin | ||
| RUN wget -q https://github.com/arq5x/bedtools2/archive/refs/tags/v${BEDTOOLS_VER}.tar.gz && \ | ||
| tar -xzf v${BEDTOOLS_VER}.tar.gz && \ | ||
| cd bedtools2-${BEDTOOLS_VER} && \ | ||
| make && \ | ||
| make install | ||
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| ### keeping old installation cmds here in case we want to install via pre-compiled binary again in the future ### | ||
| # RUN cd /usr/local/bin && \ | ||
| # wget https://github.com/arq5x/bedtools2/releases/download/v${BEDTOOLS_VER}/bedtools.static && \ | ||
| # mv bedtools.static bedtools && \ | ||
| # chmod +x bedtools && \ | ||
| # mkdir /data | ||
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| ### testing in builder ### | ||
| # test scripts expect to be run from the bedtools root dir | ||
| WORKDIR /bedtools2-${BEDTOOLS_VER} | ||
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| # commenting out ulimit command in test/test.sh (gitpod complains) | ||
| # run tests included with bedtools code | ||
| RUN sed -i 's/ulimit/#ulimit/g' test/test.sh && \ | ||
| make test | ||
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| ### final app stage ### | ||
| # starting from fresh base image instead of a previous stage | ||
| FROM ubuntu:jammy as app | ||
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| ARG BEDTOOLS_VER | ||
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| LABEL base.image="ubuntu:jammy" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="bedtools" | ||
| LABEL software.version="${BEDTOOLS_VER}" | ||
| LABEL description="bedtools - the swiss army knife for genome arithmetic" | ||
| LABEL website="https://github.com/arq5x/bedtools2" | ||
| LABEL license="https://github.com/arq5x/bedtools2/blob/master/LICENSE" | ||
| LABEL maintainer="Curtis Kapsak" | ||
| LABEL maintainer.email="[email protected]" | ||
| LABEL maintainer2="Erin Young" | ||
| LABEL maintainer2.email="[email protected]" | ||
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| # copy in all bedtools executable files from builder stage to final app stage | ||
| COPY --from=builder /usr/local/bin/* /usr/local/bin | ||
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| 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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| # setting just in case for singularity compatibility | ||
| ENV LC_ALL=C | ||
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| # default command is to print help options | ||
| CMD [ "bedtools", "--help" ] | ||
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| # set final working directory to /data | ||
| WORKDIR /data | ||
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| FROM app as test | ||
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| # check help options and version | ||
| RUN bedtools --help && \ | ||
| bedtools --version | ||
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| # downloads two bedfiles for ARTIC SARS-CoV-2 artic schemes, fixes their formatting, uses bedtools sort, intersect, and merge | ||
| RUN wget https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V5.3.2/SARS-CoV-2.primer.bed -O V5.3.2.artic.bed && \ | ||
| wget https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V4.1/SARS-CoV-2.primer.bed -O V4.1.artic.bed && \ | ||
| awk '{print $1 "\t" $2 "\t" $3 "\t" $4 "\t" $5 "\t" $6}' V5.3.2.artic.bed > V5.3.2.unsorted.bed && \ | ||
| bedtools sort -i V5.3.2.unsorted.bed > V5.3.2.bed && \ | ||
| awk '{print $1 "\t" $2 "\t" $3 "\t" $4 "\t" $5 "\t" $6}' V4.1.artic.bed > V4.1.bed && \ | ||
| bedtools intersect -a V5.3.2.bed -b V4.1.bed > intersect_test.bed && \ | ||
| mergeBed -i V5.3.2.bed > merged_test.bed && \ | ||
| head intersect_test.bed merged_test.bed |
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| # bedtools2 container | ||
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| GitHub Repo: [bedtools](https://github.com/arq5x/bedtools2/) | ||
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| Full documentation: [https://bedtools.readthedocs.io/en/latest/index.html](https://bedtools.readthedocs.io/en/latest/index.html) | ||
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| > Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line. | ||
| List of sub-commands in bedtools 2.31.0: | ||
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| - annotate | ||
| - bamtobed | ||
| - bamtofastq | ||
| - bed12tobed6 | ||
| - bedpetobam | ||
| - bedtobam | ||
| - closest | ||
| - cluster | ||
| - complement | ||
| - coverage | ||
| - expand | ||
| - flank | ||
| - fisher | ||
| - genomecov | ||
| - getfasta | ||
| - groupby | ||
| - igv | ||
| - intersect | ||
| - jaccard | ||
| - links | ||
| - makewindows | ||
| - map | ||
| - maskfasta | ||
| - merge | ||
| - multicov | ||
| - multiinter | ||
| - nuc | ||
| - overlap | ||
| - pairtobed | ||
| - pairtopair | ||
| - random | ||
| - reldist | ||
| - shift | ||
| - shuffle | ||
| - slop | ||
| - sort | ||
| - subtract | ||
| - summary | ||
| - tag | ||
| - unionbedg | ||
| - window | ||
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| ## Example Usage | ||
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| ```bash | ||
| # bedtools consists of a suite of sub-commands that are invoked as follows: | ||
| # bedtools [sub-command] [options] | ||
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| # For example, to intersect two BED files, one would invoke the following: | ||
| bedtools intersect -a a.bed -b b.bed | ||
| ``` | ||
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| More examples are found in the [bedtools tutorial](http://quinlanlab.org/tutorials/bedtools/bedtools.html) |