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Merge branch 'develop' into aa-dist-star
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ekiernan authored May 30, 2024
2 parents 101988c + eef30f3 commit f8ed3d4
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32 changes: 29 additions & 3 deletions .github/workflows/build-cutadapt.yml
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
name: Cutadapt CI

# Controls when the workflow will run
# Controls when the workflow will run.
on:
# Triggers the workflow on push or pull request events but only for the "develop" and "master" branch
pull_request:
Expand All @@ -20,12 +20,13 @@ env:
# Region-specific Google Docker repository where GOOGLE_PROJECT/REPOSITORY_NAME can be found
DOCKER_REGISTRY: us.gcr.io
GCR_PATH: broad-gotc-prod/cutadapt
ACR_PATH: cutadapt
TAG: ${{ github.event.inputs.image_tag || github.head_ref || github.ref_name }}

# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:
# The job that builds our container
build:
build-for-gcr:
runs-on: ubuntu-latest
defaults:
run:
Expand Down Expand Up @@ -56,4 +57,29 @@ jobs:
password: ${{ secrets.GCR_CI_KEY }}
# Push the image to the Google Docker registry
- name: Push image
run: "docker push ${DOCKER_REGISTRY}/${GCR_PATH}:${TAG}"
run: "docker push ${DOCKER_REGISTRY}/${GCR_PATH}:${TAG}"

build-for-acr:
runs-on: ubuntu-latest
defaults:
run:
working-directory: 3rd-party-tools/cutadapt
steps:
# checkout the repo
- name: 'Checkout GitHub Action'
uses: actions/checkout@v3

- name: 'Login via Azure CLI'
uses: azure/login@v1
with:
creds: ${{ secrets.AZURE_CREDENTIALS }}

- name: 'Build and push image'
uses: azure/docker-login@v1
with:
login-server: ${{ secrets.REGISTRY_LOGIN_SERVER }}
username: ${{ secrets.REGISTRY_USERNAME }}
password: ${{ secrets.REGISTRY_PASSWORD }}
- run: |
docker build . -t ${{ secrets.REGISTRY_LOGIN_SERVER }}/${ACR_PATH}:${TAG}
docker push ${{ secrets.REGISTRY_LOGIN_SERVER }}/${ACR_PATH}:${TAG}
30 changes: 28 additions & 2 deletions .github/workflows/build-m3c-yap-hisat.yml
Original file line number Diff line number Diff line change
Expand Up @@ -20,12 +20,13 @@ env:
# Region-specific Google Docker repository where GOOGLE_PROJECT/REPOSITORY_NAME can be found
DOCKER_REGISTRY: us.gcr.io
GCR_PATH: broad-gotc-prod/m3c-yap-hisat
ACR_PATH: m3c-yap-hisat
TAG: ${{ github.event.inputs.image_tag || github.head_ref || github.ref_name }}

# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:
# The job that builds our container
build:
build-for-gcr:
runs-on: ubuntu-latest
defaults:
run:
Expand Down Expand Up @@ -56,4 +57,29 @@ jobs:
password: ${{ secrets.GCR_CI_KEY }}
# Push the image to the Google Docker registry
- name: Push image
run: "docker push ${DOCKER_REGISTRY}/${GCR_PATH}:${TAG}"
run: "docker push ${DOCKER_REGISTRY}/${GCR_PATH}:${TAG}"

build-for-acr:
runs-on: ubuntu-latest
defaults:
run:
working-directory: 3rd-party-tools/m3c-yap-hisat
steps:
# checkout the repo
- name: 'Checkout GitHub Action'
uses: actions/checkout@v3

- name: 'Login via Azure CLI'
uses: azure/login@v1
with:
creds: ${{ secrets.AZURE_CREDENTIALS }}

- name: 'Build and push image'
uses: azure/docker-login@v1
with:
login-server: ${{ secrets.REGISTRY_LOGIN_SERVER }}
username: ${{ secrets.REGISTRY_USERNAME }}
password: ${{ secrets.REGISTRY_PASSWORD }}
- run: |
docker build . -t ${{ secrets.REGISTRY_LOGIN_SERVER }}/${ACR_PATH}:${TAG}
docker push ${{ secrets.REGISTRY_LOGIN_SERVER }}/${ACR_PATH}:${TAG}
84 changes: 84 additions & 0 deletions .github/workflows/build-plink-regenie.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,84 @@
name: PLINK2 REGENIE CI

# Controls when the workflow will run
on:
# Triggers the workflow on push or pull request events but only for the "develop" and "master" branch
pull_request:
branches: [ "develop", "master" ]
paths:
- '3rd-party-tools/plink-regenie/**'
# Allows you to run this workflow manually from the Actions tab
workflow_dispatch:
inputs:
image_tag:
description: 'Docker Image Tag (default: branch_name)'

env:
PROJECT_NAME: WARP 3rd Party Tools
# Github repo name
REPOSITORY_NAME: ${{ github.event.repository.name }}
# Region-specific Google Docker repository where GOOGLE_PROJECT/REPOSITORY_NAME can be found
DOCKER_REGISTRY: us.gcr.io
GCR_PATH: broad-gotc-prod/plink-regenie
ACR_PATH: plink-regenie
TAG: ${{ github.event.inputs.image_tag || github.head_ref || github.ref_name }}

# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:
# The job that builds our container
build-for-gcr:
runs-on: ubuntu-latest
defaults:
run:
working-directory: 3rd-party-tools/plink-regenie
# Map a step output to a job output
outputs:
imagePath: ${{ steps.saveImagePath.outputs.url }}
steps:
# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
- uses: actions/checkout@v3
- name: Build the Docker image
run: docker build . --file Dockerfile --tag ${DOCKER_REGISTRY}/${GCR_PATH}:${TAG}
- name: Check working directory'
run: |
echo "Current directory: "
pwd
ls -lht
# Save the image path to an output
- id: 'saveImagePath'
run: echo "url=${DOCKER_REGISTRY}/${GCR_PATH}:${TAG}" >> $GITHUB_OUTPUT
# Log into the Google Docker registry
- id: 'Auth'
name: Login to GCR
uses: docker/login-action@v2
with:
registry: ${{ env.DOCKER_REGISTRY }}
username: _json_key
password: ${{ secrets.GCR_CI_KEY }}
# Push the image to the Google Docker registry
- name: Push image
run: "docker push ${DOCKER_REGISTRY}/${GCR_PATH}:${TAG}"

build-for-acr:
runs-on: ubuntu-latest
defaults:
run:
working-directory: 3rd-party-tools/plink-regenie
steps:
# checkout the repo
- name: 'Checkout GitHub Action'
uses: actions/checkout@v3

- name: 'Login via Azure CLI'
uses: azure/login@v1
with:
creds: ${{ secrets.AZURE_CREDENTIALS }}
- name: 'Build and push image'
uses: azure/docker-login@v1
with:
login-server: ${{ secrets.REGISTRY_LOGIN_SERVER }}
username: ${{ secrets.REGISTRY_USERNAME }}
password: ${{ secrets.REGISTRY_PASSWORD }}
- run: |
docker build . -t ${{ secrets.REGISTRY_LOGIN_SERVER }}/${ACR_PATH}:${TAG}
docker push ${{ secrets.REGISTRY_LOGIN_SERVER }}/${ACR_PATH}:${TAG}
32 changes: 29 additions & 3 deletions .github/workflows/build-samtools-dist-bwa.yml
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
name: Samtools Dist BWA Mem 2 Ubuntu CI

# Controls when the workflow will run
# Controls when the workflow will run.
on:
# Triggers the workflow on push or pull request events but only for the "develop" and "master" branch
pull_request:
Expand All @@ -20,12 +20,13 @@ env:
# Region-specific Google Docker repository where GOOGLE_PROJECT/REPOSITORY_NAME can be found
DOCKER_REGISTRY: us.gcr.io
GCR_PATH: broad-gotc-prod/samtools-dist-bwa
ACR_PATH: samtools-dist-bwa
TAG: ${{ github.event.inputs.image_tag || github.head_ref || github.ref_name }}

# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:
# The job that builds our container
build:
build-for-gcr:
runs-on: ubuntu-latest
defaults:
run:
Expand Down Expand Up @@ -56,4 +57,29 @@ jobs:
password: ${{ secrets.GCR_CI_KEY }}
# Push the image to the Google Docker registry
- name: Push image
run: "docker push ${DOCKER_REGISTRY}/${GCR_PATH}:${TAG}"
run: "docker push ${DOCKER_REGISTRY}/${GCR_PATH}:${TAG}"

build-for-acr:
runs-on: ubuntu-latest
defaults:
run:
working-directory: 3rd-party-tools/samtools-dist-bwa
steps:
# checkout the repo
- name: 'Checkout GitHub Action'
uses: actions/checkout@v3

- name: 'Login via Azure CLI'
uses: azure/login@v1
with:
creds: ${{ secrets.AZURE_CREDENTIALS }}

- name: 'Build and push image'
uses: azure/docker-login@v1
with:
login-server: ${{ secrets.REGISTRY_LOGIN_SERVER }}
username: ${{ secrets.REGISTRY_USERNAME }}
password: ${{ secrets.REGISTRY_PASSWORD }}
- run: |
docker build . -t ${{ secrets.REGISTRY_LOGIN_SERVER }}/${ACR_PATH}:${TAG}
docker push ${{ secrets.REGISTRY_LOGIN_SERVER }}/${ACR_PATH}:${TAG}
30 changes: 28 additions & 2 deletions .github/workflows/build-snapatac2.yml
Original file line number Diff line number Diff line change
Expand Up @@ -20,12 +20,13 @@ env:
# Region-specific Google Docker repository where GOOGLE_PROJECT/REPOSITORY_NAME can be found
DOCKER_REGISTRY: us.gcr.io
GCR_PATH: broad-gotc-prod/snapatac2
ACR_PATH: snapatac2
TAG: ${{ github.event.inputs.image_tag || github.head_ref || github.ref_name }}

# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:
# The job that builds our container
build:
build-for-gcr:
runs-on: ubuntu-latest
defaults:
run:
Expand Down Expand Up @@ -56,4 +57,29 @@ jobs:
password: ${{ secrets.GCR_CI_KEY }}
# Push the image to the Google Docker registry
- name: Push image
run: "docker push ${DOCKER_REGISTRY}/${GCR_PATH}:${TAG}"
run: "docker push ${DOCKER_REGISTRY}/${GCR_PATH}:${TAG}"

build-for-acr:
runs-on: ubuntu-latest
defaults:
run:
working-directory: 3rd-party-tools/snapatac2
steps:
# checkout the repo
- name: 'Checkout GitHub Action'
uses: actions/checkout@v3

- name: 'Login via Azure CLI'
uses: azure/login@v1
with:
creds: ${{ secrets.AZURE_CREDENTIALS }}

- name: 'Build and push image'
uses: azure/docker-login@v1
with:
login-server: ${{ secrets.REGISTRY_LOGIN_SERVER }}
username: ${{ secrets.REGISTRY_USERNAME }}
password: ${{ secrets.REGISTRY_PASSWORD }}
- run: |
docker build . -t ${{ secrets.REGISTRY_LOGIN_SERVER }}/${ACR_PATH}:${TAG}
docker push ${{ secrets.REGISTRY_LOGIN_SERVER }}/${ACR_PATH}:${TAG}
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