Genomics Data Carpentry Dockerfile

Container development for Data Carpentry Genomics lessons

Draft instructions

• Docker image: https://hub.docker.com/r/jasonjwilliamsny/dc_genomics
• Docker pull command: docker pull jasonjwilliamsny/dc_genomics:dev_1.8

Setup config files

Enter usernames for your image users

1. Clone this repo and place docker-persistant/ in a convenient location on your server. In docker-persistant/ edit usernames.txt; this file should have one or more valid linux username(s) (one name per line). Accounts will be created in your container for each user. The sample list has dcuser which will be assigned the password by the script 'data4Carp'

   tip: You can edit the password in line 25 and 39 of initiate.sh

   Note: Your user will have a home directory at /home/$user This will be a symbolic link to a folder docker-persistant/$user that will be created on the machine running the docker container. In this way, data and changes made by the user on the hub will exist persistently outside of the container.

Copy docker-persistant

1. Place docker-persistant/ in a suitable location on the machine where Docker is hosted. The -v option used at execution will bind this folder.

2. Make sure /docker-persistant/initiate.sh is executable:

    chmod +x SOMEPATH/docker-persistant/initiate.sh
   

Running the container

1. Pull the image from dockerhub

    docker pull jasonjwilliamsny/dc_genomics:dev_1.8
   

2. Start the container with this command (remember to edit the location of docker-persistant/)

    docker run -p 8787:8787 -p 22:22 --name dc_genomics -d -v SOMEPATH/docker-persistant:/docker-persistant jasonjwilliamsny/dc_genomics:dev_1.8
   

3. Rstudio will be available at the ip address of the machine

    127.0.0.1:8787
    localhost:8787
   

4. SSH will be accessible at the ip address of the machine

    127.0.0.1:22
    localhost:22
   

   Login

     dcuser
     data4Carp