Bioconductor Dockers
Overview
This repository contains Dockerfiles for different Docker containers of interest for Bioconductor users. Additional information about available containers, installation and modification can be found on the Bioconductor Docker Page or Docker installation.
Available Docker Containers
See also Bioconductor Docker Page.
[email protected]:
Maintained by the Bioconductor Core Team:Docker Container | Docker Hub Latest Version | Image Size |
---|---|---|
release_base2 (GitHub) (DockerHub) | ||
release_core2 (GitHub) (DockerHub) | ||
devel_base2 (GitHub) (DockerHub) | ||
devel_core2 (GitHub) (DockerHub) |
[email protected]
Maintained by Steffen Neumann:Maintained as part of the “PhenoMeNal, funded by Horizon2020 grant 654241”
Docker Container | Docker Hub Latest Version | Image Size |
---|---|---|
release_protmetcore2 (GitHub) (DockerHub) | ||
release_metabolomics2 (GitHub) (DockerHub) | ||
devel_protmetcore2 (GitHub) (DockerHub) | ||
devel_metabolomics2 (GitHub) (DockerHub) |
[email protected]
Maintained by Laurent Gatto:Docker Container | Docker Hub Latest Version | Image Size |
---|---|---|
release_mscore2 (GitHub) (DockerHub) | ||
release_protcore2 (GitHub) (DockerHub) | ||
release_proteomics2 (GitHub) (DockerHub) | ||
devel_mscore2 (GitHub) (DockerHub) | ||
devel_protcore2 (GitHub) (DockerHub) | ||
devel_proteomics2 (GitHub) (DockerHub) |
General Docker Usage
A well organized guide to popular docker commands can be found here. For convenience, below are some commands to get you started. Note: You may need to add sudo before each command
List which docker machines are available locally
docker images
List running containers
docker ps
List all containers
docker ps -a
Get container IP address
docker inspect --format '{{ .NetworkSettings.IPAddress }}' <name>
Get a copy of public docker
docker pull <name>
Keep a container running at startup
docker run -itd <name>
Shutdown container
docker stop <name>
Resume container
docker start <name>
Delete container
docker rm <name>
Shell into a running container with either of the following:
docker exec -it <name> /bin/bash
docker attach <name>
Building and modifying the Bioconductor docker images
The BioC Dockerfiles are not directly edited. Instead,
for each biocView, there is a common Dockerfile.in
,
from which two output files for release
and devel
files are generated by running
the rake
command. All the creation is controlled by the Rakefile
,
which will also take care if any of the dependencies (i.e. the *.in files) have changed.
E.g. the Dockerfile
for the BioC development branch for core packages
is created from src/core/Dockerfile.in
and placed into
out/devel_core/Dockerfile
.