Using Docker with Seven Bridges Genomics (SBG) CGC - Part 1

Install Docker

https://docs.docker.com/engine/installation/
There are many ways of installing Docker. Go to the url above for installation details.

I installed Docker using “Homebrew” on my mac.

brew install docker
brew install docker-machine

Using Docker with SB CGC

docker-machine ls

#if you do not have host named "dev"
docker-machine create --driver virtualbox dev
#if you have a host named "dev
docker-machine start dev

docker-machine regenerate-certs dev
docker-machine env dev
eval "$(docker-machine env dev)"

docker-machine stop dev
docker-machine rm dev

The Hello-world example

To check your installation, pull and run the hello-world image from the docker respository.
You should see a “Hello from Docker” message, which confirms that docker is installed correctly.

docker pull hello-world
docker images
docker run hello-world

A simple example creating a tool in Ubuntu using the CGC image registry

This tutorial assumes that you are familiar with the basics of Seven Bridges CGC.
If not, please check out http://teamcgc.nci.nih.gov.s3-website-us-east-1.amazonaws.com/

In this example, we will use the unix command “grep” to look for a string (“KX”) in a input FASTA file and print the line containing that string in an output file

Input FASTA file content

>gb:KU991811|Organism:Zika virus Brazil/2016/INMI1-Asian|Segment:null|Subtype:Asian|Host:Human
MKNPKKKSGGFRIVNMLKRGVARVSPFGGLKRLPAGLLLGHGPI

>gb:KU955590|Organism:Zika virus Z16019-Asian|Segment:null|Subtype:Asian|Host:Human
MKNPKKKSGGFRIVNMLKRGVARVSPFGGLKRLPAGLLLGHGPI

>gb:KU922960|Organism:Zika virus MEX/InDRE/Sm/2016-Asian|Segment:null|Subtype:Asian|Host:Human
MKNPKKKSGGFRIVNMLKRGVARVSPFGGLKRLPAGLLLGHGPI

>gb:KX056898|Organism:Zika virus Zika virus/GZ02/2016-Asian|Segment:null|Subtype:Asian|Host:Human
MKNPKKKSGGFRIVNMLKRGVARVSPFGGLKRLPAGLLLGHGPI

>gb:KU922923|Organism:Zika virus MEX/InDRE/Lm/2016-Asian|Segment:null|Subtype:Asian|Host:Human
MKNPKKKSGGFRIVNMLKRGVARVSPFGGLKRLPAGLLLGHGPI

>gb:KU963574|Organism:Zika virus ZIKV/Homo sapiens/NGA/IbH-30656_SM21V1-V3/1968-West_African|Segment:null|Subtype:West_African|Host:Human
MKNPKKKSGGFRIVNMLKRGVARVNPLGGLKRLPAGLLLGHGPI

We will create a tool with the latest Ubuntu image in the CGC registry to search the above input file for a sequence header containing the string “KX”



Under “GENERAL” - Login to your CGC account
- Click on the “Apps” tab
- Click on “+Add app”
- Click on “Create Tool”
- Enter a name for the tool “ubuntu-grep”, Click “Create”
- Enter “ubuntu:latest” in the Docker Repository field
- Enter “grep” in the Base Command field
- Enter “output.txt”
This creates a tool that will pull the latest Ubuntu image from the CGC register, run the “grep” command and create an output file named “output.txt”



Under “INPUTS” - Create 3 input ports by clicking on the “+” sign. You want the resulting command line to look like -
“grep ‘string_pattern’ input_file > output.txt”
grep (base command) is position 0 in the command line
‘string pattern’ is position 1 in the command line
input_file is position 2 in the command line



Under “OUTPUTS” - Create an output port by clicking on “+”



Under “TEST” You can enter different names different ports and see if the resulting command line looks right - Click on “SAVE” - Click on “RUN” to start a task with this tool


Under “Set Input Data” - Click on “Pick files” to select the input file



Under “Define App Settings” - Enter the name of the output file and the string/pattern you want to search in the input file - Click “Run” and confirm


Task being queued and waiting to run



You should see the output file under “Files” In the output file (output.txt), you should see the header line containing the string “KX”

>gb:KX056898|Organism:Zika virus Zika virus/GZ02/2016-Asian|Segment:null|Subtype:Asian|Host:Human