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* adding bakta version 1.9.4 * Update Dockerfile micromamba clean -a -f -y --------- Co-authored-by: Kutluhan Incekara <[email protected]>
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FROM mambaorg/micromamba:1.5.8 as app | ||
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ARG BAKTA_VER="1.9.4" | ||
ARG DIAMOND_VER="2.1.8" | ||
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# 'LABEL' instructions tag the image with metadata that might be important to the user | ||
LABEL base.image="mambaorg/micromamba:1.5.8" | ||
LABEL dockerfile.version="1" | ||
LABEL software="Bakta" | ||
LABEL software.version="${BAKTA_VER}" | ||
LABEL description="rapid & standardized annotation of bacterial genomes, MAGs & plasmids" | ||
LABEL website="https://github.com/oschwengers/bakta" | ||
LABEL license="https://github.com/oschwengers/bakta/blob/main/LICENSE" | ||
LABEL maintainer="Erin Young" | ||
LABEL maintainer.email="[email protected]" | ||
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USER root | ||
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RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
wget \ | ||
procps \ | ||
ca-certificates && \ | ||
apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
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RUN micromamba install --name base -c conda-forge -c bioconda -c defaults bakta=${BAKTA_VER} diamond=${DIAMOND_VER} && \ | ||
micromamba clean -a -f -y && \ | ||
mkdir /data | ||
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ENV PATH="/opt/conda/bin/:$PATH" \ | ||
LC_ALL=C | ||
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CMD bakta --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 bakta --help && \ | ||
bakta_db --help && \ | ||
bakta --version | ||
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RUN bakta_db list && \ | ||
bakta_db download --type light | ||
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RUN wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/195/815/GCF_000195815.1_ASM19581v1/GCF_000195815.1_ASM19581v1_genomic.fna.gz && \ | ||
gunzip GCF_000195815.1_ASM19581v1_genomic.fna.gz && \ | ||
bakta --db /test/db-light GCF_000195815.1_ASM19581v1_genomic.fna && \ | ||
head GCF_000195815.1_ASM19581v1_genomic.gbff |
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# bakta container | ||
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Main tool: [bakta](https://github.com/oschwengers/bakta) | ||
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Code repository: https://github.com/oschwengers/bakta | ||
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Basic information on how to use this tool: | ||
- executable: bakta | ||
- help: -h | ||
- version: -v | ||
- description: Annotates bacterial genomes | ||
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> Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs. It provides dbxref-rich, sORF-including and taxon-independent annotations in machine-readable JSON & bioinformatics standard file formats for automated downstream analysis. | ||
Additional information: | ||
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WARNING : Image does not contain a database. | ||
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Full documentation: https://github.com/oschwengers/bakta/ | ||
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## Example Usage | ||
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```bash | ||
bakta sample.fasta --db <path to database> --threads 20 --prefix sample | ||
``` |