Adding bakta light (#868)

* adding light

* adding light to README

* Rename Dockerfile to Dockerfile

* Rename README.md to README.md

* Update README.md to reflect directory change

README.md

@@ -115,7 +115,7 @@ 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) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/artic-ncov2019-nanopolish)](https://hub.docker.com/r/staphb/artic-ncov2019-nanopolish) | <ul><li>1.1.0</ul> | https://github.com/artic-network/artic-ncov2019 |
 | [Augur](https://github.com/nextstrain/augur) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/augur)](https://hub.docker.com/r/staphb/augur) | <ul><li>6.3.0</li><li>7.0.2</li><li>8.0.0</li><li>9.0.0</li><li>16.0.3</li></ul> | https://github.com/nextstrain/augur |
 | [Auspice](https://hub.docker.com/r/staphb/auspice) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/auspice)](https://hub.docker.com/r/staphb/auspice) | <ul><li>2.12.0</li></ul> | https://github.com/nextstrain/auspice |
-| [bakta](https://hub.docker.com/r/staphb/bakta) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bakta)](https://hub.docker.com/r/staphb/bakta) | <ul><li>[1.9.2](./bakta/1.9.2/)</li></ul> | https://github.com/oschwengers/bakta |
+| [bakta](https://hub.docker.com/r/staphb/bakta) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bakta)](https://hub.docker.com/r/staphb/bakta) | <ul><li>[1.9.2](./bakta/1.9.2/)</li><li>[1.9.2-light](./bakta/1.9.2-5.1-light/)</li></ul> | https://github.com/oschwengers/bakta |
 | [BBTools](https://hub.docker.com/r/staphb/bbtools/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bbtools)](https://hub.docker.com/r/staphb/bbtools) | <ul><li>38.76</li><li>38.86</li><li>38.95</li><li>38.96</li><li>38.97</li><li>38.98</li><li>38.99</li><li>39.00</li><li>39.01</li></ul> | https://jgi.doe.gov/data-and-tools/bbtools/ |
 | [bcftools](https://hub.docker.com/r/staphb/bcftools/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bcftools)](https://hub.docker.com/r/staphb/bcftools) | <ul><li>[1.10.2](./bcftools/1.10.2/)</li><li>[1.11](./bcftools/1.11/)</li><li>[1.12](./bcftools/1.12/)</li><li>[1.13](./bcftools/1.13/)</li><li>[1.14](./bcftools/1.14/)</li><li>[1.15](./bcftools/1.15/)</li><li>[1.16](./bcftools/1.16/)</li><li>[1.17](./bcftools/1.17/)</li><li>[1.18](bcftools/1.18/)</li><li>[1.19](./bcftools/1.19/)</li></ul> | https://github.com/samtools/bcftools |
 | [bedtools](https://hub.docker.com/r/staphb/bedtools/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bedtools)](https://hub.docker.com/r/staphb/bedtools) | <ul><li>2.29.2</li><li>2.30.0</li><li>[2.31.0](bedtools/2.31.0/)</li><li>[2.31.1](bedtools/2.31.1/)</li></ul> | https://bedtools.readthedocs.io/en/latest/ <br/>https://github.com/arq5x/bedtools2 |

bakta/1.9.2-5.1-light/Dockerfile

@@ -0,0 +1,54 @@
+FROM mambaorg/micromamba:1.4.9 as app
+
+ARG BAKTA_VER="1.9.2"
+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:1.4.9"
+LABEL dockerfile.version="1"
+LABEL software="Bakta"
+LABEL software.version="${BAKTA_VER}"
+LABEL description="rapid & standardized annotation of bacterial genomes, MAGs & plasmids"
+LABEL website="https://github.com/oschwengers/bakta"
+LABEL license="https://github.com/oschwengers/bakta/blob/main/LICENSE"
+LABEL maintainer="Erin Young"
+LABEL maintainer.email="[email protected]"
+
+USER root
+
+WORKDIR /
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    procps \
+    ca-certificates && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+RUN micromamba install --name base -c conda-forge -c bioconda -c defaults bakta=${BAKTA_VER} diamond=${DIAMOND_VER} && \
+    micromamba clean -a -y && \
+    mkdir /data
+
+ENV PATH="/opt/conda/bin/:$PATH" \
+    LC_ALL=C \
+    BAKTA_DB=/db/db-light
+
+WORKDIR /db
+
+RUN bakta_db download --type light 
+
+CMD bakta --help
+
+WORKDIR /data
+
+FROM app as test
+
+WORKDIR /test
+
+RUN bakta --help && \
+    bakta_db --help && \
+    bakta --version
+
+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 GCF_000195815.1_ASM19581v1_genomic.fna && \
+    head GCF_000195815.1_ASM19581v1_genomic.gbff

bakta/1.9.2-5.1-light/README.md

@@ -0,0 +1,24 @@
+# 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:
+
+This image contains the version 5.1 light database. It is located in /db/db-light and set as BAKTA_DB so that --db doesn't have to be used.
+
+Full documentation: https://github.com/oschwengers/bakta/
+
+Example Usage
+```bash
+bakta sample.fasta --threads 20 --prefix sample 
+```