From adedd567d0f526b40dec836c29de75ede28a2cb0 Mon Sep 17 00:00:00 2001 From: Samuel Lee Date: Mon, 20 Oct 2025 08:42:48 -0400 Subject: [PATCH 1/5] Testing non-MKL BLAS for gCNV. --- scripts/gatkcondaenv.yml.template | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/gatkcondaenv.yml.template b/scripts/gatkcondaenv.yml.template index 51d00ce99e8..38b5af5ab5d 100644 --- a/scripts/gatkcondaenv.yml.template +++ b/scripts/gatkcondaenv.yml.template @@ -23,7 +23,7 @@ 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 # 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 From 282e38041cf4fd1583cd693b6a299f1c549f2239 Mon Sep 17 00:00:00 2001 From: samuelklee Date: Thu, 23 Oct 2025 10:42:02 -0400 Subject: [PATCH 2/5] Update gatkcondaenv.yml.template --- scripts/gatkcondaenv.yml.template | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/scripts/gatkcondaenv.yml.template b/scripts/gatkcondaenv.yml.template index 38b5af5ab5d..64e029afaaa 100644 --- a/scripts/gatkcondaenv.yml.template +++ b/scripts/gatkcondaenv.yml.template @@ -26,17 +26,17 @@ dependencies: - conda-forge:blas # 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::pytensor +- conda-forge::scipy - conda-forge::h5py=3.10.0 -- conda-forge::pytorch=2.1.0=*mkl*100 +- conda-forge::pytorch - 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 - conda-forge::pandas=2.1.3 - conda-forge::tqdm=4.66.1 - conda-forge::dill=0.3.7 # used for pickling lambdas in TrainVariantAnnotationsModel -- conda-forge::biopython=1.84 # used by NVScoreVariants +- conda-forge::biopython. # used by NVScoreVariants # core R dependencies; these should only be used for plotting and do not take precedence over core python dependencies! - r-base=4.3.1 From 956a0f35e9bb6479b6af79cc160167e10b84c789 Mon Sep 17 00:00:00 2001 From: samuelklee Date: Thu, 23 Oct 2025 11:00:09 -0400 Subject: [PATCH 3/5] Update gatkcondaenv.yml.template --- scripts/gatkcondaenv.yml.template | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/gatkcondaenv.yml.template b/scripts/gatkcondaenv.yml.template index 64e029afaaa..2ae036edf7f 100644 --- a/scripts/gatkcondaenv.yml.template +++ b/scripts/gatkcondaenv.yml.template @@ -36,7 +36,7 @@ dependencies: - conda-forge::pandas=2.1.3 - conda-forge::tqdm=4.66.1 - conda-forge::dill=0.3.7 # used for pickling lambdas in TrainVariantAnnotationsModel -- conda-forge::biopython. # used by NVScoreVariants +- conda-forge::biopython # used by NVScoreVariants # core R dependencies; these should only be used for plotting and do not take precedence over core python dependencies! - r-base=4.3.1 From 27529f032f23e0662fcd9eb2834aa7f9671c21bb Mon Sep 17 00:00:00 2001 From: Samuel Lee Date: Mon, 27 Oct 2025 13:30:04 -0400 Subject: [PATCH 4/5] Reverted version numbers in conda YML. --- scripts/gatkcondaenv.yml.template | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/scripts/gatkcondaenv.yml.template b/scripts/gatkcondaenv.yml.template index 2ae036edf7f..9ea95f57bbc 100644 --- a/scripts/gatkcondaenv.yml.template +++ b/scripts/gatkcondaenv.yml.template @@ -23,20 +23,20 @@ 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 # 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 -- conda-forge::scipy +- conda-forge::pytensor=2.18.3 +- conda-forge::scipy=1.11.4 - conda-forge::h5py=3.10.0 -- conda-forge::pytorch +- 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 - conda-forge::pandas=2.1.3 - conda-forge::tqdm=4.66.1 - conda-forge::dill=0.3.7 # used for pickling lambdas in TrainVariantAnnotationsModel -- conda-forge::biopython # used by NVScoreVariants +- conda-forge::biopython=1.84 # used by NVScoreVariants # core R dependencies; these should only be used for plotting and do not take precedence over core python dependencies! - r-base=4.3.1 From e3722447a9895e63cf217e3fd7f5422cd3075353 Mon Sep 17 00:00:00 2001 From: Samuel Lee Date: Mon, 27 Oct 2025 13:31:46 -0400 Subject: [PATCH 5/5] Changed test runner to ubuntu-24.04-arm. --- .github/workflows/gatk-tests.yml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/.github/workflows/gatk-tests.yml b/.github/workflows/gatk-tests.yml index 31b9bb1fc68..c57d3b33f88 100644 --- a/.github/workflows/gatk-tests.yml +++ b/.github/workflows/gatk-tests.yml @@ -26,7 +26,7 @@ jobs: 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: @@ -37,7 +37,7 @@ jobs: 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 @@ -71,7 +71,7 @@ jobs: #Run our non-docker tests test: - runs-on: ubuntu-latest + runs-on: ubuntu-24.04-arm needs: check-secrets strategy: matrix: @@ -145,7 +145,7 @@ jobs: #Run our docker tests testOnDocker: needs: [buildDocker, check-secrets] - runs-on: ubuntu-latest + runs-on: ubuntu-24.04-arm strategy: matrix: java: [ 17.0.6+10 ] @@ -245,7 +245,7 @@ jobs: #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 @@ -266,7 +266,7 @@ jobs: #run wdl validation on generated WDLs generatedWdlValidation: - runs-on: ubuntu-latest + runs-on: ubuntu-24.04-arm name: Validate generated WDLs using womtools steps: - uses: actions/checkout@v3 @@ -288,7 +288,7 @@ jobs: #Run our various targeted medium scale wdl wiring tests wdlTests: - 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' ]