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* initial Dockerfile * adding drprg 0.1.1 * attempted downloading index at new location * added htslib * working version * made lowercase
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| # 'FROM' defines the base docker image. This command has to come first in the file | ||
| # The 'as' keyword lets you name the folowing stage. The production image uses everything to the 'app' stage. | ||
| FROM mambaorg/micromamba:1.5.1 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 DRPRG_VER="0.1.1" | ||
| ARG MTB_VER="20230308" | ||
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| # build and run as root users since micromamba image has 'mambauser' set as the $USER | ||
| USER root | ||
| # set workdir to default for building; set to /data at the end | ||
| WORKDIR / | ||
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| # 'LABEL' instructions tag the image with metadata that might be important to the user | ||
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| LABEL base.image="mambaorg/micromamba:1.4.9" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="Dr. PRG" | ||
| LABEL software.version="${DRPRG_VER}" | ||
| LABEL description="Antimicrobial resistance prediction" | ||
| LABEL website="https://github.com/mbhall88/drprg" | ||
| LABEL license="https://github.com/mbhall88/drprg/blob/main/LICENSE" | ||
| LABEL maintainer="Erin Young" | ||
| LABEL maintainer.email="[email protected]" | ||
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| # 'RUN' executes code during the build | ||
| # Install dependencies via apt-get or yum if using a centos or fedora base | ||
| RUN apt-get update && apt-get install --no-install-recommends -y \ | ||
| wget \ | ||
| ca-certificates \ | ||
| procps && \ | ||
| rm -rf /var/lib/apt/lists/* && apt-get autoclean | ||
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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 drprg=${DRPRG_VER} && \ | ||
| micromamba clean -a -y && \ | ||
| mkdir /data | ||
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| # 'ENV' instructions set environment variables that persist from the build into the resulting image | ||
| # set the environment, add base conda/micromamba bin directory into path | ||
| # set locale settings to UTF-8 | ||
| ENV PATH="/opt/conda/bin/:${PATH}" \ | ||
| LC_ALL=C.UTF-8 | ||
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| # download MTB index and change the name | ||
| RUN mkdir /drprg && \ | ||
| drprg index --download mtb@${MTB_VER} --outdir /drprg && \ | ||
| mv /drprg/mtb/mtb-${MTB_VER} /drprg/mtb/mtb | ||
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| CMD drprg --help | ||
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| WORKDIR /data | ||
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| FROM app as test | ||
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| WORKDIR /test | ||
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| RUN drprg --help | ||
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| # testing prediction | ||
| RUN wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR230/005/SRR23086705/SRR23086705_1.fastq.gz && \ | ||
| drprg predict -x /drprg/mtb/mtb -i SRR23086705_1.fastq.gz --illumina -o outdir/ && \ | ||
| ls outdir/* | ||
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| # list available databases for download | ||
| RUN drprg index --list |
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| <!-- | ||
| Please edit this readme with some basic information about the tool and how to use this container. | ||
| - Include information about databases and additional files that are included. | ||
| - Keep it short - you don't need to recreate the documentation from the creators. | ||
| - Do not just copy and paste the readme or help for the tool. | ||
| --> | ||
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| # Dr. PRG - Drug resistance Prediction with Reference Graphs️ container | ||
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| Main tool: [Dr. PRG](https://mbh.sh/drprg/) | ||
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| Code repository: https://github.com/mbhall88/drprg | ||
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| Basic information on how to use this tool: | ||
| - executable: drprg | ||
| - help: --help | ||
| - version: --version | ||
| - description: Drug Resistance Prediction with Reference Graphs | ||
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| Additional information: | ||
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| Imagine contains the mtb@20230308 database located at `/drprg/mtb/mtb`. | ||
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| Full documentation: https://mbh.sh/drprg/guide/download.html | ||
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| ## Example Usage | ||
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| Using the index in from the image | ||
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| ```bash | ||
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| # prediction (paired-end fastq files much be contatenated together into one) | ||
| drprg predict -x /drprg/mtb/mtb -i input.fastq.gz --illumina -o outdir/ | ||
| ``` | ||
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| Getting the latest index and using it | ||
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| ```bash | ||
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| # download latest TB database | ||
| drprg index --download mtb | ||
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| # list available indices | ||
| drprg index --list | ||
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| # prediction (paired-end fastq files much be contatenated together into one) | ||
| drprg predict -x mtb -i input.fastq.gz --illumina -o outdir/ | ||
| ``` |