Update package versions in Docker images. #816
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mwalker174
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Jul 2, 2025
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| # You may speed up the compilation of htslib, bcftools, and vcftools by | ||
| # parallelizing the build process. You may dynamically choose thread count | ||
| # at runtime using: -j $(nproc --all) | ||
| # However, that runs into uncommon error (maybe race condition) with the | ||
| # following error message: | ||
| # > collect2: error: ld returned 1 exit status | ||
| # | ||
| # While running with a single-thread is slower, but the process is more | ||
| # reproducible and reliable. You may override the following argument | ||
| # and be mindful of the above possible error. | ||
| ARG THREAD_COUNT="1" |
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In my experience, -j often leads to problems except in the simplest of projects
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Exactly, I was running into those issues, so I set the thread count to 1. But we can also remove that option altogether if we're ok with disabling parallel make.
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We are updating Docker images to (a) build base-off the current latest build of Ubuntu 22.04 (22.04.5), and (b) the current latest version of some of the packages installed in the images. The goal is to minimize vulnerabilities in GATK-SV docker images, hence, the updates are scoped to only those dependencies flagged by GCP's artifact registry scan and include only the dependencies with vulnerability severity above "medium."