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mmorgantaylor committed Mar 15, 2024
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10 changes: 5 additions & 5 deletions 3rd-party-tools/beagle/README.md
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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.
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The Imputation Beagle image uses the following convention for versioning:

#### `us.gcr.io/broad-gotc-prod/samtools:<image-version>-<beagle-version>-<unix-timestamp>`
#### `us-central1-docker.pkg.dev/morgan-fieldeng-gcp/imputation-beagle-development/imputation-beagle:<image-version>-<beagle-version>-<manual-timestamp>`

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
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```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
```
2 changes: 2 additions & 0 deletions 3rd-party-tools/beagle/docker_build.sh
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Expand Up @@ -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
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