Slim Docker images for bioinformatics tools built on Alpine Linux (mostly).
Build a single image:
docker build --no-cache -t imagename
Push to Docker Hub:
# docker login
docker tag imagename username/imagename
docker push username/imagename
Build all images:
USERNAME="stephenturner"
echo '#!/bin/bash' > BUILD.sh
find . -type f -name "Dockerfile" -exec dirname {} \; \
| sort \
| sed 's/\.\///g' \
| xargs -I{} echo "docker build --no-cache -t ${USERNAME}/{} {}/" \
>> BUILD.sh
bash build.sh
Run an executable from the image mounting the local current working directory to /data:
docker run --rm -u $(id -u):$(id -g) -v $(pwd):$(pwd) -w $(pwd) imagename
Create an alias to make this a little easier. Put this in your ~/.bashrc:
function docker_run { docker run --rm -u $(id -u):$(id -g) -v $(pwd):$(pwd) -w $(pwd) "$@"; }
Then:
docker_run imagename
Run multiple piped commands inside the container. Example with bcftools assuming example.vcf.gz lives in the current working directory:
docker run --rm -u $(id -u):$(id -g) -v $(pwd):$(pwd) -w $(pwd) --entrypoint /bin/ash stephenturner/bcftools -c \
"bcftools view -r 1 example.vcf.gz | bcftools query -f '%CHROM\t%POS\t[%TGT]\n'"
Step inside a container:
docker run --rm -it --entrypoint /bin/ash imagename
docker pull stephenturner/minimap2