From 00c769a2fa2fdc75e298bde9078cbce6bd12ba70 Mon Sep 17 00:00:00 2001 From: Morgan Taylor Date: Fri, 15 Mar 2024 13:51:41 -0400 Subject: [PATCH] updates --- 3rd-party-tools/beagle/README.md | 10 +++++----- 3rd-party-tools/beagle/docker_build.sh | 2 ++ 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/3rd-party-tools/beagle/README.md b/3rd-party-tools/beagle/README.md index 64f556fe..a0bdc7b8 100644 --- a/3rd-party-tools/beagle/README.md +++ b/3rd-party-tools/beagle/README.md @@ -4,7 +4,7 @@ Copy and paste to pull this image -#### `us.gcr.io/broad-gotc-prod/imputation-beagle:0.0.1-01Mar24.d36-xxxx` +#### `us-central1-docker.pkg.dev/morgan-fieldeng-gcp/imputation-beagle-development/imputation-beagle:0.0.1-01Mar24.d36-wip-temp-20240301` - __What is this image:__ This image is a lightweight alpine-based image for running Beagle in the [ImputationBeagle pipeline](../../../../pipelines/broad/arrays/imputation_beagle/ImputationBeagle.wdl). - __What is Beagle:__ Beagle is a software package for phasing genotypes and imputing ungenotyped markers. Beagle version 5.4 has improved memory and computational efficiency when analyzing large sequence data sets. See [here](https://faculty.washington.edu/browning/beagle/beagle.html) for more information. @@ -14,15 +14,15 @@ Copy and paste to pull this image The Imputation Beagle image uses the following convention for versioning: -#### `us.gcr.io/broad-gotc-prod/samtools:--` +#### `us-central1-docker.pkg.dev/morgan-fieldeng-gcp/imputation-beagle-development/imputation-beagle:--` We keep track of all past versions in [docker_versions](docker_versions.tsv) with the last image listed being the currently used version in WARP. You can see more information about the image, including the tool versions, by running the following command: ```bash -$ docker pull us.gcr.io/broad-gotc-prod/imputation-beagle:0.0.1-01Mar24.d36-xxxx -$ docker inspect us.gcr.io/broad-gotc-prod/imputation-beagle:0.0.1-01Mar24.d36-xxxx +$ docker pull us-central1-docker.pkg.dev/morgan-fieldeng-gcp/imputation-beagle-development/imputation-beagle:0.0.1-01Mar24.d36-wip-temp-20240301 +$ docker inspect us-central1-docker.pkg.dev/morgan-fieldeng-gcp/imputation-beagle-development/imputation-beagle:0.0.1-01Mar24.d36-wip-temp-20240301 ``` ## Usage @@ -31,5 +31,5 @@ $ docker inspect us.gcr.io/broad-gotc-prod/imputation-beagle:0.0.1-01Mar24.d36-x ```bash $ docker run --rm -it \ - us.gcr.io/broad-gotc-prod/imputation-beagle:0.0.1-1.0.2-1663948783 /usr/gitc/beagle + us-central1-docker.pkg.dev/morgan-fieldeng-gcp/imputation-beagle-development/imputation-beagle:0.0.1-01Mar24.d36-wip-temp-20240301 /usr/gitc/beagle ``` \ No newline at end of file diff --git a/3rd-party-tools/beagle/docker_build.sh b/3rd-party-tools/beagle/docker_build.sh index 32491745..1d9ac7c1 100755 --- a/3rd-party-tools/beagle/docker_build.sh +++ b/3rd-party-tools/beagle/docker_build.sh @@ -63,6 +63,8 @@ function main(){ IMAGE_TAG="$DOCKER_IMAGE_VERSION-$BEAGLE_VERSION-$TIMESTAMP" echo "building and pushing GCR Image - $GAR_URL:$IMAGE_TAG" + + # TODO: add `--squash` when ready to productionize. https://docs.docker.com/reference/cli/docker/image/build/#squash docker build -t "$GAR_URL:$IMAGE_TAG" \ --build-arg BEAGLE_VERSION="$BEAGLE_VERSION" \ $DIR