From 8ede20a336f6fded6490e1fbfacbf5663932d996 Mon Sep 17 00:00:00 2001 From: phendriksen100 <103142505+phendriksen100@users.noreply.github.com> Date: Wed, 21 Feb 2024 16:25:22 -0500 Subject: [PATCH 1/6] add cutadapt --- .github/workflows/build-cutadapt.yml | 30 ++++++++++++++++++++++++++-- 1 file changed, 28 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build-cutadapt.yml b/.github/workflows/build-cutadapt.yml index 96cd6427..1eda4830 100644 --- a/.github/workflows/build-cutadapt.yml +++ b/.github/workflows/build-cutadapt.yml @@ -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: @@ -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}" \ No newline at end of file + 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} \ No newline at end of file From 58c8a1414f570ef2cb72b490ca6c95b0b8b0fcc0 Mon Sep 17 00:00:00 2001 From: phendriksen100 <103142505+phendriksen100@users.noreply.github.com> Date: Wed, 21 Feb 2024 16:31:27 -0500 Subject: [PATCH 2/6] add samtools dist --- .github/workflows/build-samtools-dist-bwa.yml | 30 +++++++++++++++++-- 1 file changed, 28 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build-samtools-dist-bwa.yml b/.github/workflows/build-samtools-dist-bwa.yml index 058cefc2..3003c10c 100644 --- a/.github/workflows/build-samtools-dist-bwa.yml +++ b/.github/workflows/build-samtools-dist-bwa.yml @@ -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: @@ -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}" \ No newline at end of file + 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} \ No newline at end of file From ecdd2bb8b52b21f1e0363984bf31b3bdf266f4f6 Mon Sep 17 00:00:00 2001 From: phendriksen100 <103142505+phendriksen100@users.noreply.github.com> Date: Wed, 21 Feb 2024 16:35:28 -0500 Subject: [PATCH 3/6] add acr for snapatac2 --- .github/workflows/build-snapatac2.yml | 30 +++++++++++++++++++++++++-- 1 file changed, 28 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build-snapatac2.yml b/.github/workflows/build-snapatac2.yml index 0630ad89..c4c31601 100644 --- a/.github/workflows/build-snapatac2.yml +++ b/.github/workflows/build-snapatac2.yml @@ -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: @@ -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}" \ No newline at end of file + 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} \ No newline at end of file From c34ec5087ed0424a763bec40b1a69776b7a5dde8 Mon Sep 17 00:00:00 2001 From: phendriksen100 <103142505+phendriksen100@users.noreply.github.com> Date: Thu, 22 Feb 2024 09:16:13 -0500 Subject: [PATCH 4/6] remove snapatac2 as it is already in narehs pr --- .github/workflows/build-snapatac2.yml | 30 ++------------------------- 1 file changed, 2 insertions(+), 28 deletions(-) diff --git a/.github/workflows/build-snapatac2.yml b/.github/workflows/build-snapatac2.yml index c4c31601..0630ad89 100644 --- a/.github/workflows/build-snapatac2.yml +++ b/.github/workflows/build-snapatac2.yml @@ -20,13 +20,12 @@ 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-for-gcr: + build: runs-on: ubuntu-latest defaults: run: @@ -57,29 +56,4 @@ 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}" - - 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} \ No newline at end of file + run: "docker push ${DOCKER_REGISTRY}/${GCR_PATH}:${TAG}" \ No newline at end of file From 3e443657379fa3032dc4d7e88d3fd61deaa13aff Mon Sep 17 00:00:00 2001 From: phendriksen100 <103142505+phendriksen100@users.noreply.github.com> Date: Thu, 22 Feb 2024 14:16:35 -0500 Subject: [PATCH 5/6] small change to make builds run --- .github/workflows/build-cutadapt.yml | 2 +- .github/workflows/build-samtools-dist-bwa.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build-cutadapt.yml b/.github/workflows/build-cutadapt.yml index 1eda4830..e924d711 100644 --- a/.github/workflows/build-cutadapt.yml +++ b/.github/workflows/build-cutadapt.yml @@ -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: diff --git a/.github/workflows/build-samtools-dist-bwa.yml b/.github/workflows/build-samtools-dist-bwa.yml index 3003c10c..9b29dae4 100644 --- a/.github/workflows/build-samtools-dist-bwa.yml +++ b/.github/workflows/build-samtools-dist-bwa.yml @@ -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: From f3ab3a760312b82a210a40781c151650a30381aa Mon Sep 17 00:00:00 2001 From: phendriksen100 <103142505+phendriksen100@users.noreply.github.com> Date: Thu, 22 Feb 2024 15:52:51 -0500 Subject: [PATCH 6/6] force run --- 3rd-party-tools/cutadapt/Dockerfile | 2 +- 3rd-party-tools/samtools-dist-bwa/Dockerfile | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/3rd-party-tools/cutadapt/Dockerfile b/3rd-party-tools/cutadapt/Dockerfile index aca18d05..d37a0bcb 100644 --- a/3rd-party-tools/cutadapt/Dockerfile +++ b/3rd-party-tools/cutadapt/Dockerfile @@ -1,4 +1,4 @@ -# Adding a platform tag to ensure that images built on ARM-based machines doesn't break pipelines +# Adding a platform tag to ensure that images built on ARM-based machines doesn't break pipelines. FROM --platform=linux/amd64 python:3.7.7 LABEL maintainer="DSP Data Centers " diff --git a/3rd-party-tools/samtools-dist-bwa/Dockerfile b/3rd-party-tools/samtools-dist-bwa/Dockerfile index 5b558ce6..f26d612f 100644 --- a/3rd-party-tools/samtools-dist-bwa/Dockerfile +++ b/3rd-party-tools/samtools-dist-bwa/Dockerfile @@ -1,4 +1,4 @@ -# Adding a platform tag to ensure that images built on ARM-based machines doesn't break pipelines +# Adding a platform tag to ensure that images built on ARM-based machines doesn't break pipelines. FROM --platform="linux/amd64" ubuntu:22.04 ENV TERM=xterm-256color