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Testing non-MKL BLAS for gCNV. #9290

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adedd56
Testing non-MKL BLAS for gCNV.
samuelklee Oct 20, 2025
282e380
Update gatkcondaenv.yml.template
samuelklee Oct 23, 2025
956a0f3
Update gatkcondaenv.yml.template
samuelklee Oct 23, 2025
27529f0
Reverted version numbers in conda YML.
samuelklee Oct 27, 2025
e372244
Changed test runner to ubuntu-24.04-arm.
samuelklee Oct 27, 2025
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14 changes: 7 additions & 7 deletions .github/workflows/gatk-tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@
name: check if the environment has privileges
outputs:
google-credentials: ${{ steps.google-credentials.outputs.defined }}
runs-on: ubuntu-latest
runs-on: ubuntu-24.04-arm
steps:
- id: google-credentials
env:
Expand All @@ -37,7 +37,7 @@

buildDocker:
name: build and push gatk docker to artifacts
runs-on: ubuntu-latest
runs-on: ubuntu-24.04-arm
steps:
- name: checkout gatk
uses: actions/checkout@v3
Expand Down Expand Up @@ -71,81 +71,81 @@

#Run our non-docker tests
test:
runs-on: ubuntu-latest
runs-on: ubuntu-24.04-arm
needs: check-secrets
strategy:
matrix:
java: [ 17.0.6+10 ]
experimental: [ false ]
scalaVersion: [ 2.13 ]
testType: [ cloud, integration, unit ]
fail-fast: false
continue-on-error: ${{ matrix.experimental }}
env:
TEST_TYPE: ${{ matrix.testType }}
SCALA_VERSION: ${{ matrix.scalaVersion }}
name: ${{ matrix.testType }} build and test Java ${{ matrix.Java }}
steps:
- uses: actions/checkout@v3
with:
fetch-depth: 0
- uses: ./.github/actions/purge-runner-disk
- name: 'Set up java ${{ matrix.Java }}'
uses: actions/setup-java@v3
with:
java-version: ${{ matrix.Java }}
distribution: 'temurin'
cache: gradle

- name: 'Compile with Gradle'
run: |
./gradlew compileJava ; ./gradlew installDist

#Google Cloud stuff
- id: 'gcloud-auth'
if: needs.check-secrets.outputs.google-credentials == 'true'
uses: google-github-actions/auth@v0
with:
credentials_json: ${{ secrets.GCP_CREDENTIALS }}
project_id: ${{ env.HELLBENDER_TEST_PROJECT }}
create_credentials_file: true

- name: "export the credentials for GATK tests"
if: needs.check-secrets.outputs.google-credentials == 'true'
run: echo "HELLBENDER_JSON_SERVICE_ACCOUNT_KEY=${{ steps.auth.outputs.credentials_file_path }}" >> $GITHUB_ENV

- name: 'Set up Cloud SDK'
if: needs.check-secrets.outputs.google-credentials == 'true'
uses: google-github-actions/setup-gcloud@v2

- name: pull lfs files
run: git lfs pull

- name: compile test code
run: ./gradlew compileTestJava

- name: run-tests
if: ${{ needs.check-secrets.outputs.google-credentials == 'true' || matrix.testType != 'cloud'}}
id: jacoco-tests
run: |
./gradlew --daemon -Dscala.version=${{ env.SCALA_VERSION }} jacocoTestReport

- uses: ./.github/actions/upload-gatk-test-results
if: always()
with:
warnPR: ${{ github.event_name == 'pull_request' && steps.jacoco-tests.outcome != 'success' }}
repo-token: ${{ secrets.GITHUB_TOKEN }}
job-matrix-id: ${{ github.run_id }}.1${{ strategy.job-index }}
repo-path: ${{ github.ref_name }}_${{ github.run_id }}.1${{ strategy.job-index }}
bot-comment-key: ${{ secrets.GATK_BOT_COMMENT_KEY }}
identifier: Java ${{ matrix.Java }} build and test ${{ matrix.testType }}
only-artifact: ${{ needs.check-secrets.outputs.google-credentials != 'true' }}


#Run our docker tests
testOnDocker:

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needs: [buildDocker, check-secrets]
runs-on: ubuntu-latest
runs-on: ubuntu-24.04-arm
strategy:
matrix:
java: [ 17.0.6+10 ]
Expand Down Expand Up @@ -245,108 +245,108 @@

#run wdl validation on WDLs in the scripts directory
scriptsWdlValidation:
runs-on: ubuntu-latest
runs-on: ubuntu-24.04-arm
name: Validate script WDLs using womtools
steps:
- uses: actions/checkout@v3
with:
fetch-depth: 0
- uses: ./.github/actions/purge-runner-disk
- name: Set up java 17
uses: actions/setup-java@v3
with:
java-version: '17'
distribution: 'temurin'
cache: gradle
- uses: ./.github/actions/install-cromwell
with:
CROMWELL_VERSION: ${{ env.CROMWELL_VERSION }}
- name: Run Scripts WDL Validation Test
run: ./gradlew gatkValidateScriptsWdl

#run wdl validation on generated WDLs
generatedWdlValidation:

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runs-on: ubuntu-latest
runs-on: ubuntu-24.04-arm
name: Validate generated WDLs using womtools
steps:
- uses: actions/checkout@v3
with:
fetch-depth: 0
- uses: ./.github/actions/purge-runner-disk
- name: Set up java 17
uses: actions/setup-java@v3
with:
java-version: '17'
distribution: 'temurin'
cache: gradle
- uses: ./.github/actions/install-cromwell
with:
CROMWELL_VERSION: ${{ env.CROMWELL_VERSION }}

- name: Run Generated WDL Validation Test
run: ./gradlew gatkValidateGeneratedWdl

#Run our various targeted medium scale wdl wiring tests
wdlTests:

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runs-on: ubuntu-latest
runs-on: ubuntu-24.04-arm
strategy:
matrix:
wdlTest: [ 'RUN_CNV_GERMLINE_COHORT_WDL', 'RUN_CNV_GERMLINE_CASE_WDL', 'RUN_CNV_SOMATIC_WDL', 'RUN_M2_WDL', 'RUN_VCF_SITE_LEVEL_FILTERING_WDL' ]
continue-on-error: true
name: WDL test ${{ matrix.wdlTest }} on cromwell
steps:
- uses: actions/checkout@v3
with:
fetch-depth: 0
- uses: ./.github/actions/purge-runner-disk
- name: pull lfs files
run: git lfs pull
- name: Set up java 17
uses: actions/setup-java@v3
with:
java-version: '17'
distribution: 'temurin'
cache: gradle
- uses: ./.github/actions/install-cromwell
with:
CROMWELL_VERSION: ${{ env.CROMWELL_VERSION }}

- name: "Exporting Environment Variables for Wdl Scripts"
run: |
if [[ "${{ github.event_name }}" == "pull_request" ]]
then
echo "CI_PULL_REQUEST=${{ github.event.number }}" >> $GITHUB_ENV
fi
echo "CI_COMMIT=${{ github.sha }}" >> $GITHUB_ENV

- name: "CNV_GERMLINE_COHORT_WDL_TEST"
if: ${{ matrix.wdlTest == 'RUN_CNV_GERMLINE_COHORT_WDL' }}
run: |
echo "Running CNV germline cohort workflow";
bash scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh COHORT;

- name: "CNV_GERMLINE_CASE_WDL_TEST"
if: ${{ matrix.wdlTest == 'RUN_CNV_GERMLINE_CASE_WDL' }}
run: |
echo "Running CNV germline case workflow";
bash scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh CASE;

- name: "CNV_SOMATIC_WDL_TEST"
if: ${{ matrix.wdlTest == 'RUN_CNV_SOMATIC_WDL' }}
run: |
echo "Running CNV somatic workflows";
bash scripts/cnv_cromwell_tests/somatic/run_cnv_somatic_workflows.sh;

- name: "M2_WDL_TEST"
if: ${{ matrix.wdlTest == 'RUN_M2_WDL' }}
run: |
echo "Deleting some unused files before running M2 WDL...";
rm -Rf src/test/resources/large/VQSR;
echo "Running M2 WDL";
bash scripts/m2_cromwell_tests/run_m2_wdl.sh;

- name: "VCF_SITE_LEVEL_FILTERING_WDL_TEST"
if: ${{ matrix.wdlTest == 'RUN_VCF_SITE_LEVEL_FILTERING_WDL' }}
run: |
echo "Running VCF Site Level Filtering WDL";
bash scripts/vcf_site_level_filtering_cromwell_tests/run_vcf_site_level_filtering_wdl.sh;

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4 changes: 2 additions & 2 deletions scripts/gatkcondaenv.yml.template
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Original file line number Diff line number Diff line change
Expand Up @@ -23,13 +23,13 @@ dependencies:
# core python dependencies
- conda-forge::python=3.10.13 # do not update without good reason
- conda-forge:pip=23.3.1
- conda-forge:blas=1.0=mkl # our official environment uses MKL versions of various packages; if other versions are desired, users should edit this YML accordingly
- conda-forge:blas=1.0 # our official environment uses MKL versions of various packages; if other versions are desired, users should edit this YML accordingly
- conda-forge::numpy=1.26.2
- conda-forge::pymc=5.10.1
- conda-forge::pytensor=2.18.3
- conda-forge::scipy=1.11.4
- conda-forge::h5py=3.10.0
- conda-forge::pytorch=2.1.0=*mkl*100
- conda-forge::pytorch=2.1.0
- conda-forge::pytorch-lightning=2.4.0 # supports Pytorch >= 2.1 and <= 2.4, used by NVScoreVariants
- conda-forge::scikit-learn=1.3.2
- conda-forge::matplotlib=3.8.2
Expand Down
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