adding bakta version 1.9.4 (#1034)

* adding bakta version 1.9.4

* Update Dockerfile

micromamba clean -a -f -y

---------

Co-authored-by: Kutluhan Incekara <[email protected]>

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) <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://hub.docker.com/r/staphb/augur) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/augur)](https://hub.docker.com/r/staphb/augur) | <ul><li>[6.3.0](./augur/6.3.0/)</li><li>[7.0.2](./augur/7.0.2/)</li><li>[8.0.0](./augur/8.0.0/)</li><li>[9.0.0](./augur/9.0.0/)</li><li>[16.0.3](./augur/16.0.3/)</li><li>[24.2.2](./augur/24.2.2/)</li><li>[24.2.3](./augur/24.2.3/)</li><li>[24.3.0](./augur/24.3.0/)</li><li>[24.4.0](./augur/24.4.0/)</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><li>[1.9.2-light](./bakta/1.9.2-5.1-light/)</li><li>[1.9.3](./bakta/1.9.3/)</li><li>[1.9.3-light](./bakta/1.9.3-5.1-light/)</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><li>[1.9.3](./bakta/1.9.3/)</li><li>[1.9.3-light](./bakta/1.9.3-5.1-light/)</li><li>[1.9.4](./bakta/1.9.4/)</li></ul> | https://github.com/oschwengers/bakta |
 | [bandage](https://hub.docker.com/r/staphb/bandage) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bandage)](https://hub.docker.com/r/staphb/bandage) | <ul><li>[0.8.1](./bandage/0.8.1/)</li></ul> | https://rrwick.github.io/Bandage/ |
 | [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](./bbtools/38.76/)</li><li>[38.86](./bbtools/38.86/)</li><li>[38.95](./bbtools/38.95/)</li><li>[38.96](./bbtools/38.96/)</li><li>[38.97](./bbtools/38.97/)</li><li>[38.98](./bbtools/38.98/)</li><li>[38.99](./bbtools/38.99/)</li><li>[39.00](./bbtools/39.00/)</li><li>[39.01](./bbtools/39.01/)</li><li>[39.06](./bbtools/39.06/)</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><li>[1.20](./bcftools/1.20/)</li><li>[1.20.c](./bcftools/1.20.c/)</li></ul> | https://github.com/samtools/bcftools |

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="${BAKTA_VER}"
+LABEL description="rapid & standardized annotation of bacterial genomes, MAGs & plasmids"
+LABEL website="https://github.com/oschwengers/bakta"
+LABEL license="https://github.com/oschwengers/bakta/blob/main/LICENSE"
+LABEL maintainer="Erin Young"
+LABEL maintainer.email="[email protected]"
+
+USER root
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    procps \
+    ca-certificates && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+RUN micromamba install --name base -c conda-forge -c bioconda -c defaults bakta=${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

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 <path to database> --threads 20 --prefix sample
+```