A collection of commonly used bioinformatics tools used for analyzing RNA-seq, ChIP-seq, and DNA-seq data.
These instructions will get you a copy of the project up and running on your local machine for development and testing purposes.
What things you need to install the software and how to install them:
docker
: https://docs.docker.com/install/git
: https://git-scm.com/book/en/v2/Getting-Started-Installing-Git
If you are unsure if you have git
or docker
installed, please type which docker
or which git
.
A step by step series of examples that tell you how to get a development environment up and running
Let's start off by cloning this repository
$ git clone https://github.com/skchronicles/Docker.git
$ cd Docker
Let's take a peak
$ tree .
.
├── ccbr_meme_suite
│ ├── Dockerfile
│ ├── README
│ └── meme-5.0.4.tar.gz
├── ccbr_python
│ ├── Dockerfile
│ └── README
└── ccbr_rsem_merge
├── Dockerfile
└── README
Each of the listed ccbr
directories represents a dockerized tool.
Within each directory you will find a REAME
and a dockerfile
. The README
contains instructions for how to build
, tag
, and push
the docker images.
# See listing of images on computer
docker image ls
# Build Dockerfile (assumes you are in the directory with the Dockerfile)
docker build --tag=ccbr_meme_suite:v0.0.1 .
# Peak around the container: verify things run correctly (similiar to `singularity shell`)
docker run -ti ccbr_meme_suite:v0.0.1 /bin/bash
echo $PATH
ls -larth /data/
ls -larth /opt/
# Check out what ever you want
exit
# Updating Tag(s) before pushing to DockerHub: create a version tag and `latest` tag
## Creating Tags for `skchronicles` account
docker tag ccbr_meme_suite:v0.0.1 skchronicles/ccbr_meme_suite:v0.0.1
docker tag ccbr_meme_suite:v0.0.1 skchronicles/ccbr_meme_suite # latest
## Creating Tags for `nciccbr` account
docker tag ccbr_meme_suite:v0.0.1 nciccbr/ccbr_meme_suite:v0.0.1
docker tag ccbr_meme_suite:v0.0.1 nciccbr/ccbr_meme_suite # latest
# Check out new tag(s)
docker image ls
# Push new tagged image to DockerHub
docker push skchronicles/ccbr_meme_suite:v0.0.1
docker push skchronicles/ccbr_meme_suite:latest
docker push nciccbr/ccbr_meme_suite:v0.0.1
docker push nciccbr/ccbr_meme_suite:latest
# To pull the image we created using docker:
docker pull nciccbr/ccbr_meme_suite
# To pull the image we created using singularity:
singularity pull docker://nciccbr/ccbr_meme_suite
We use git
, GitHub
, and DockerHub
for versioning. For the versions available on GitHub, please see the tags on this repository.
For more information about available container images, please visit: