Docker

A collection of commonly used bioinformatics tools used for analyzing RNA-seq, ChIP-seq, and DNA-seq data.

Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes.

Prerequisites

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.

Installation

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.

README: ccbr_meme_suite

# 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

Versioning

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: