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adding bakta version 1.9.3 (#914)
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* adding bakta version 1.9.3

* Updated micromamba version to 1.5.7
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erinyoung authored Mar 19, 2024
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -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></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></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></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</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 |
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52 changes: 52 additions & 0 deletions bakta/1.9.3/Dockerfile
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FROM mambaorg/micromamba:1.5.7 as app

ARG BAKTA_VER="1.9.3"
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:1.5.7"
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 -y && \
mkdir /data

ENV PATH="/opt/conda/bin/:$PATH" \
LC_ALL=C

CMD bakta --help

WORKDIR /data

FROM app as test

#export BAKTA_DB=/test/db-light

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
25 changes: 25 additions & 0 deletions bakta/1.9.3/README.md
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# 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
```

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