streptomyces/andy_asgbk repository overview

⁠extract_from_gbk.pl

⁠Downloading the image from Docker Hub.

First pull the container from Docker Hub.

docker pull streptomyces/andy_asgbk

⁠Using

Put all your genbank files in a directory and cd to the directory which contains this directory. In the examples below I am assuming that you have named the directory containing your genbank files as gbk.

The Docker image has the ENTRYPOINT set to the Perl script extract_from_gbk.pl. This means that you can run the image and it will automatically run the script in a container. Any arguments you pass to the docker run command after the name of the image will be passed to the Perl script. Once the script is done the container will be removed automatically because of the --rm option.

The -v ${PWD}:/home/work will bind-mount your current directory on your computer to the /home/work directory in the running container.

docker run --rm -v ${PWD}:/home/work \
streptomyces/andy_asgbk -indir gbk -outfile out.faa \
-type "lanthipeptide-class-v: HopA1"

There are three options and all three are required with no default values.

⁠-indir

The name of the directory containing the genbank files.

⁠-type

The string (actually a regular expression) to look for in the gene_functions tags.

⁠-outfile

The name of the fasta file to which the selected protein sequences are written. If this file exists it will be overwritten.

⁠Notes for Govind. Users to ignore.

Built on lin9

Dockerfile, script and README.md are in /home/sco/mnt/scratch/docker/andy/2024_08_14.

docker buildx build --load --no-cache \
-t streptomyces/andy_asgbk:latest -f Dockerfile .

docker buildx build --platform linux/amd64,linux/arm64 \
--no-cache -t streptomyces/andy_asgbk:latest \
--push -f Dockerfile .

Testing in /home/sco/mnt/scratch/andy/2024_08_15 where there is a gbk directory.