TSPS-222 Docker setup for Beagle Imputation WDL #114
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mmorgantaylor
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mmorgantaylor
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Feb 20, 2025
| # Registries and tags | ||
| GCR_URL="us.gcr.io/broad-gotc-prod/imputation-beagle" | ||
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| # GAR setup |
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todo: clean this up
mmorgantaylor
commented
Feb 20, 2025
| set -e | ||
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| # Update version when changes to Dockerfile are made | ||
| DOCKER_IMAGE_VERSION=0.0.2 # TODO UPDATE TO 1.0.0 WHEN READY |
mmorgantaylor
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jsotobroad
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Feb 24, 2025
| @@ -0,0 +1,2 @@ | |||
| us.gcr.io/broad-gotc-prod/imputation-beagle:0.0.2-17Dec24.224-1739986611 | |||
| us.gcr.io/broad-gotc-prod/imputation-beagle:1.0.0-17Dec24.224-1740423035 | |||
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i think we can jsut have one version here
| rm bcftools-${BCFTOOLS_VERSION}.tar.bz2 \ | ||
| ; \ | ||
| # Download Beagle jars | ||
| # beagle runs phasing and imputation |
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comment spacing is a little weird. are these indented comments useful or should these be in like the readme instead?
3rd-party-tools/beagle/Dockerfile
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| # bref3 converts a reference panel from vcf to the bref3 format that Beagle needs | ||
| curl -L https://faculty.washington.edu/browning/beagle/bref3.${BREF3_VERSION}.jar > bref3.${BREF3_VERSION}.jar \ | ||
| ; \ | ||
| # Install tini |
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| chmod +x /sbin/tini; | ||
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| # Set tini as default entrypoint | ||
| ENTRYPOINT ["/sbin/tini", "--" ] |
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just cuz i like being annoying - is this necessary?
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jsotobroad
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Feb 24, 2025
nikellepetrillo
approved these changes
Feb 25, 2025
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Docker image for ImputationBeagle - used with PR #1333 in warp
Jira ticket: https://broadworkbench.atlassian.net/browse/TSPS-222