Build the sv-base docker using GATK released images instead of compiling from the given commit

[VJalili]

Affected module(s) or script(s)

• sv-base docker image

Description

The sv-base docker image is built by compiling GATK from a particular git commit, which is motivated by the need for the un-merged/un-released tool PrintSVEvidence. This tool is used in multiple workflows.

gatk-sv/dockerfiles/sv-base/Dockerfile

Lines 27 to 34 in 902a319

	RUN git clone https://github.com/broadinstitute/gatk.git && \
	cd gatk && \
	git lfs install && \
	git checkout ${GATK_COMMIT}
	# build GATK_JAR
	RUN cd gatk && \
	./gradlew localJar && \
	mv $(readlink -f build/libs/gatk.jar) ${GATK_JAR}

Building the sv-base docker image as above has a few drawbacks that impede the image build on the GitHub actions.

• It requires a full git history checkout at cloning to check out the particular commit. The full git history checkout of GATK is a slow operation on Github runners
• Pulling LFS-tracked files results in downloading ~14GB data, which is (a) a very slow operation on Github runners, and (b) leads to out-of-disk issues.

Downloading LFS-tracked files, full history cloning together with compiling/building of GATK, adds to the total runtime of building docker images, resulting in over 6h of runtime on Github actions for building all the Docker images, which is force-killed by Github.

Building sv-base leveraging released GATK docker images can potentially alleviate the building challenges, which will require updating workflows and docker images where PrintSVEvidence is needed. Maybe the latter can be addressed as part of #324.