docker-dragen

Resources

https://www.illumina.com/products/by-type/informatics-products/dragen-bio-it-platform.html

Dragen home page

https://support.illumina.com/sequencing/sequencing_software/dragen-bio-it-platform/downloads.html

Dragen software downloads

Build

To build a different version, see Versions below.

NOTE: As of Dragen 4.0.3, Illumina provide a stable URL for the run file instead of a timed signed URL to a zip file. See Build (old) below for how it used to work. This stable URL is hard-coded in the Dockerfile so no additional modifications are needed.

Build the Docker image

# You will see errors because the Dragen package is 
# being installed away from the Dragen itself. It will still work.
make build

Launch an interactive shell

make interact

push to DockerHub (be sure to modify Makefile to use your own account)

make push

Build (old)

Download Dragen software 3.8.4 (Centos 7) from

https://support.illumina.com/sequencing/sequencing_software/dragen-bio-it-platform/downloads.html

When you click on the download link a signed URL that can be used on the command line will be provided. This link should replace URL in Dockerfile in the line

RUN wget -O dragen-3.8.4-7.el7.x86_64.zip 'URL' && \

And proceed as in build. Note that the old way used a signed URL The R build can take so long that the signed link will expire; if so, get a new signed link and the build will start where it left off and the link should work.

Versions

Be sure to get the Centos 7 version of whatever Dragen version you are downloading (as of 3.8.x, this is the only option).

The build instructions are for version 3.8.4, the latest version as of 20210707. To use a different version, change the version number in the Makefile from

VERSION := 3.8.4

to match the version in the name of the zip file. For example, version 3.7.5 should be set to

VERSION := 3.7.5

This is necessary for correct Docker image tagging. Essential is to change the commands in the Dockerfile to match the downloaded filename. For example, 3.7.5 has a zip file named

dragen-3.7.5-4.el7.x86_64.zip

So the following should be all be changed from

wget -O dragen-3.8.4-7.el7.x86_64.zip
...
unzip dragen-3.8.4-7.el7.x86_64.zip && \
rm -f dragen-3.8.4-7.el7.x86_64.zip && \
/bin/sh dragen-3.8.4-7.el7.x86_64.run; \

wget -O dragen-3.7.5-4.el7.x86_64.zip
...
unzip dragen-3.7.5-4.el7.x86_64.zip && \
rm -f dragen-3.7.5-4.el7.x86_64.zip && \
/bin/sh dragen-3.7.5-4.el7.x86_64.run; \

Usage

Dragen software is installed under /opt/edico.

The dragen binary

/opt/edico/bin/dragen

when run with no arguments will print a help message, but note that if run away from the Dragen hardware it will result in a driver error instead.

A note on Dockerfile installs

The image is large, in part because of the requirements installed in the Docker image. I tried to come up with a minimal set for a successful build of 3.7.5 by letting the Dragen install fail on missing packages and adding them one by one. This set continues to work for 3.8.4 and 4.0.3