Download GATK4 required packages in docker container
Hello, I have installed GATK4 (version 4.4.0) in a docker container in MacOS following the published instructions (https://gatk.broadinstitute.org/hc/en-us/articles/360035889991). I also created a link to the reads and reference data outside the container (mount volume). Everything works fine, but the additional packages (fastqc, bwa) are are not in the pulled docker image, and I have been trying to figure out how to install them inside the container to have all the packages in one place. Is that possible?
Thank you, Marcela
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Hello,
We don't include every package in our docker image but if you're comfortable with docker it's not hard to make your own image based on ours. There are at least two ways.
1. Run our docker image interactively,
docker run -it broadinstitute/gatk:4.4.0.0
Then install the tools you want, and then in another shell (outside of the docker instance) on the same machine you can use `docker commit` and save the new image with a new name. This is the easiest way to get started but it's a pain because if you want to move to a newer version of gatk you have to do it again manually.2. The better way which will take a few more steps and some trial and error is to create a new dockerfile that uses our image as the base and add stuff to it. Basically make a new docker file that starts with importing the GATK docker you want to base your new image on.
FROM broadinstitute/gatk:4.4.0.0
RUN: apt-get install bwa ... //your installs hereThen you can build that docker file and make a new image you can use. The benefit here is that if you want to rebuild it with a new gatk you can just change the import line.
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