gerbenvoshol / Dragen

Run Dragen as a container

Playing around Dragen Server

Karim Mezhoud 2023-02-23

Dockerize Dragen

This Quick Start deploys Dynamic Read Analysis for GENomics Suite (DRAGEN CS), a data analysis platform by Illumina, on CentOS/ORACLE Linux/Clonezilla OSs.

How to extract dragen-x.x.x.el8.x86_64.run file

The installer file like dragen-4.0.3-8.el8.x86_64.run is composed by 3 files:

• edico_driver-1.4.7-4.0.3.el8.x86_64.rpm,
• edico-4.0.3-15.el8.x86_64.rpm, and
• installer.

Parsing Nirvana Json file to tibble

 

 

 

Visualize Dragen FastQC Report

 

 

 

Create Docker image from .ISO file

The goal is to use/convert ORACLE/CentOS/Clonezilla .ISO image as a docker container.

sudo apt-get install squashfs-tools -y
wget -P ~/Download/ https://webdata.illumina.com/downloads/software/clonezilla/clonezilla-live-40.0.C11.20221017.RAID_OL8_CF.iso
mkdir rootfs unsqushfs
# To mount the ISO image into the rootfs folder 
sudo mount -o loop ~/Download/clonezilla-live-40.0.C11.20221017.RAID_OL8_CF.iso ~/rootfs
# We need to locate the directory housing of the filesystem.squashfs file. 
cd ~/rootfs
# locate the file
find . -type f | grep filesystem.squashfs
#The file is locate at ./live/filesystem.squashfs
cd ..
## we can extract the necessary filesystem files from the rootfs directory into the unsquashfs directory 
sudo unsquashfs -f -d unsquashfs/ rootfs/live/filesystem.squashfs

# Finally, we can compress and import the image using Docker
sudo tar -C unsquashfs -c . | docker import - ol8_illumina:latest

# list docker image
docker image ls

ol8_illumina           latest    fe075c356df2   3 minutes ago   1.14GB

Customize ol8_illumina image with Dragen installer, ssh access and others needed tools

go to same folder where the Dockerfile and run the two commands. There ar two option to run the container: interactively or detached. In the same folder we need dragen-4.0.3-8.el8.x86_64.run installer that you can get from illumina download page.

docker build -t ol8_ill_drag_el8:latest .
# run it interactively (-i)
#you will prompted directly  to container terminal
# root@ol8_illu_drag_el8:/home_dragen
docker run -h ol8_illu_drag_el8 -i -t ol8_illu_drag_el8:latest bash

#or detach the container from the terminal -d
docker run -dit --name dragen ol8_illu_drag_el8:latest

# list running container 
docker container ls

CONTAINER ID   IMAGE                      COMMAND                  CREATED          STATUS          PORTS     NAMES
d7553c21ea9a   ol8_illu_drag_el8:latest   "/bin/sh -c 'service…"   29 seconds ago   Up 28 seconds             dragen

To execute command from running container

docker exec -it dragen ls

To attach the running container

docker attach dragen