diff --git a/README.md b/README.md index 967ac14d0..212440df5 100644 --- a/README.md +++ b/README.md @@ -116,7 +116,7 @@ To learn more about the docker pull rate limits and the open source software pro | [artic-ncov2019-nanopolish](https://hub.docker.com/r/staphb/artic-ncov2019-nanopolish)
[![docker pulls](https://badgen.net/docker/pulls/staphb/artic-ncov2019-nanopolish)](https://hub.docker.com/r/staphb/artic-ncov2019-nanopolish) | | https://github.com/artic-network/artic-ncov2019 | | [Augur](https://hub.docker.com/r/staphb/augur)
[![docker pulls](https://badgen.net/docker/pulls/staphb/augur)](https://hub.docker.com/r/staphb/augur) | | https://github.com/nextstrain/augur | | [Auspice](https://hub.docker.com/r/staphb/auspice)
[![docker pulls](https://badgen.net/docker/pulls/staphb/auspice)](https://hub.docker.com/r/staphb/auspice) | | https://github.com/nextstrain/auspice | -| [bakta](https://hub.docker.com/r/staphb/bakta)
[![docker pulls](https://badgen.net/docker/pulls/staphb/bakta)](https://hub.docker.com/r/staphb/bakta) | | https://github.com/oschwengers/bakta | +| [bakta](https://hub.docker.com/r/staphb/bakta)
[![docker pulls](https://badgen.net/docker/pulls/staphb/bakta)](https://hub.docker.com/r/staphb/bakta) | | https://github.com/oschwengers/bakta | | [bandage](https://hub.docker.com/r/staphb/bandage)
[![docker pulls](https://badgen.net/docker/pulls/staphb/bandage)](https://hub.docker.com/r/staphb/bandage) | | https://rrwick.github.io/Bandage/ | | [BBTools](https://hub.docker.com/r/staphb/bbtools/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/bbtools)](https://hub.docker.com/r/staphb/bbtools) | | https://jgi.doe.gov/data-and-tools/bbtools/ | | [bcftools](https://hub.docker.com/r/staphb/bcftools/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/bcftools)](https://hub.docker.com/r/staphb/bcftools) | | https://github.com/samtools/bcftools | diff --git a/bakta/1.9.4/Dockerfile b/bakta/1.9.4/Dockerfile new file mode 100644 index 000000000..982da23a0 --- /dev/null +++ b/bakta/1.9.4/Dockerfile @@ -0,0 +1,50 @@ +FROM mambaorg/micromamba:1.5.8 as app + +ARG BAKTA_VER="1.9.4" +ARG DIAMOND_VER="2.1.8" + +# '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="${BAKTA_VER}" +LABEL description="rapid & standardized annotation of bacterial genomes, MAGs & plasmids" +LABEL website="https://github.com/oschwengers/bakta" +LABEL license="https://github.com/oschwengers/bakta/blob/main/LICENSE" +LABEL maintainer="Erin Young" +LABEL maintainer.email="eriny@utah.gov" + +USER root + +RUN apt-get update && apt-get install -y --no-install-recommends \ + wget \ + procps \ + ca-certificates && \ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +RUN micromamba install --name base -c conda-forge -c bioconda -c defaults bakta=${BAKTA_VER} diamond=${DIAMOND_VER} && \ + micromamba clean -a -f -y && \ + mkdir /data + +ENV PATH="/opt/conda/bin/:$PATH" \ + LC_ALL=C + +CMD bakta --help + +WORKDIR /data + +FROM app as test + +WORKDIR /test + +RUN bakta --help && \ + bakta_db --help && \ + bakta --version + +RUN bakta_db list && \ + bakta_db download --type light + +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 diff --git a/bakta/1.9.4/README.md b/bakta/1.9.4/README.md new file mode 100644 index 000000000..255820db5 --- /dev/null +++ b/bakta/1.9.4/README.md @@ -0,0 +1,25 @@ +# bakta container + +Main tool: [bakta](https://github.com/oschwengers/bakta) + +Code repository: https://github.com/oschwengers/bakta + +Basic information on how to use this tool: +- executable: bakta +- help: -h +- version: -v +- description: Annotates bacterial genomes + +> 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: + +WARNING : Image does not contain a database. + +Full documentation: https://github.com/oschwengers/bakta/ + +## Example Usage + +```bash +bakta sample.fasta --db --threads 20 --prefix sample +```