Dockerfile

Host the dockerfile from dockerhub/delhomme

Content

Sorted in dependencies order:

• Command line based:

1. upscb-jbrowse

2. upscb-ngs-preprocessing

3. upscb-chipseq and upscb-rnaseq

• R and R-studio based

1. upscb-r-base
2. upscb-rstudio
3. upscb-rstudio-sequencing

• Others:

1. upscb-nodejs

Installation

If you do not have docker installed; do ( on a linux distro)

curl https://get.docker.com | sh
sudo usermod -a -G docker ubuntu
sudo service docker start

Then simply clone the present repository, cd into the docker you want to build and do e.g.:

git clone https://github.com/UPSCb/Dockerfile.git
cd delhomme/upscb-jbrowse
docker build -t delhomme/upscb-jbrowse

Or if you do not want to build it on your system, but just pull it

docker pull  delhomme/upscb-jbrowse

Details

Linux based containers

upscb-jbrowse

Create the user training from the group training with password training and install JBrowse in /var/www/html. JBrowse is not configured. To provide access to JBrowse you need to map the container port 80; e.g. here is the run command that will start the docker and map port 80 on port 9001

docker run -d -p 9001:80 delhomme/upscb-jbrowse

upscb-ngs-preprocessing

Build on the previous, contains all the tools necessary to run the pre-processing of RNA-Seq data as described in our guidelines: http://www.epigenesys.eu/en/protocols/bio-informatics/1283-guidelines-for-rna-seq-data-analysis. The tools are:

• FastQC
• SortMeRNA
• Trimmomatic
• MultiQC

This container also installs GateOne, a terminal emulator for the web browser, and expose the corresponding necessary port 443. It also expose the ssh port 22.

The following command is an example to run it that maps 443 to 10001 and 22 to 11001.

docker run -d -p 9001:80 -p 10001:443 -p 11001:22 delhomme/upscb-jbrowse

upscb-chipseq and upscb-rnaseq

These two depends on the previous one and expose the same ports. They contain tools necessary to do ChIP-Seq and RNA-Seq analysis respectively, i.e.

• R
• HTSlib
• BEDTools
• BWA
• MACS2
• USeq
• Sissrs

and

• HTSlib
• STAR
• HTSeq
• kallisto

respectively.

R and R-studio based

1. upscb-r-base Simply install base R and create the user training from the group training with password training. The default R installation directory is configured to be /home/training/.r-library.

2. upscb-rstudio Install RStudio server (the non-commercial edition). It exposes port 8787 (web browser access to RStudio). Here is the run command that will start the docker and map port 8787 on port 12001

docker run -d -p 12001:8787 delhomme/upscb-r-studio

3. upscb-rstudio-sequencing Build on the above, installing all the necessary R/Bioconductor packages for the analysis of RNA-Seq data.

Others

1. upscb-nodejs

   A simple container containing a git checkout of our nodejs website used for courses and workshops.

Some more docker commands

• to list the images docker images

• to remove images docker rmi [image ID]

• to list containers docker ps -a

• to stop a container docker stop [container ID]

• to remove a container docker rm [container ID]

• both in oneline docker rm $(docker stop [container ID])

• to connect to a container as root, activating some terminal support docker exec -ti [container ID] env TERM=xterm bash