Fix Glimpse docker failure

.github/workflows/run_tests.yaml

@@ -9,14 +9,16 @@ on:
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
+env:
+  CROMWELL_VERSION: 91
 jobs:
   validate_wdl:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
       - uses: ./.github/actions/install-cromwell
         with:
-          CROMWELL_VERSION: 89
+          CROMWELL_VERSION: ${{ env.CROMWELL_VERSION }}
       - name: Womtool Validate
         run: find . -name '*.wdl' | xargs -tI {} java -jar ${WOMTOOL_JAR} validate {}
 
@@ -36,7 +38,7 @@ jobs:
           service_account: palantir-workflows-service-acc@broad-dsde-methods.iam.gserviceaccount.com
       - uses: ./.github/actions/install-cromwell
         with:
-          CROMWELL_VERSION: 89
+          CROMWELL_VERSION: ${{ env.CROMWELL_VERSION }}
       - uses: ./.github/actions/install-watt
         with:
           WATT_VERSION: v1.4.0

GlimpseImputationPipeline/Glimpse2Imputation.wdl

@@ -23,7 +23,7 @@ workflow Glimpse2Imputation {
         Int? effective_population_size
 
         Int preemptible = 9
-        String docker = "us.gcr.io/broad-dsde-methods/glimpse:odelaneau_bd93ade"
+        String docker = "us.gcr.io/broad-dsde-methods/glimpse:odelaneau_f72ff67"
         String docker_extract_num_sites_from_reference_chunk = "us.gcr.io/broad-dsde-methods/glimpse_extract_num_sites_from_reference_chunks:michaelgatzen_edc7f3a"
         Int cpu_ligate = 4
         Int mem_gb_ligate = 4
@@ -161,7 +161,7 @@ task GlimpsePhase {
     command <<<
         set -euo pipefail
 
-        export GCS_OAUTH_TOKEN=$(/root/google-cloud-sdk/bin/gcloud auth application-default print-access-token)
+        export GCS_OAUTH_TOKEN=$(/google-cloud-sdk/bin/gcloud auth application-default print-access-token)
 
         cram_paths=( ~{sep=" " crams} )
         cram_index_paths=( ~{sep=" " cram_indices} )

GlimpseImputationPipeline/glimpse_docker/Dockerfile

@@ -21,7 +21,11 @@ rm -r bcftools-1.16
 RUN wget https://github.com/broadinstitute/picard/releases/download/2.26.11/picard.jar && \
 mv picard.jar /
 
+WORKDIR /
 # Install gcloud
-RUN curl -sSL https://sdk.cloud.google.com | bash
+RUN curl -O https://dl.google.com/dl/cloudsdk/channels/rapid/downloads/google-cloud-cli-linux-x86_64.tar.gz && \
+tar -xzf google-cloud-cli-linux-x86_64.tar.gz && \
+./google-cloud-sdk/install.sh -q --path-update True && \
+rm google-cloud-cli-linux-x86_64.tar.gz
 
-WORKDIR /
+RUN rm -r /docker_build/

GlimpseImputationPipeline/glimpse_docker/build_base_and_extension_docker.sh

@@ -2,7 +2,7 @@
 
 # This branch is using the following configuration.
 # To replicate this branch, run this script with the following arguments:
-# build_base_and_extension_docker.sh -r "https://github.com/kachulis/GLIMPSE.git" -b ck_checkpoint_clean -t "glimpse_build_test"
+# build_base_and_extension_docker.sh -r "https://github.com/odelaneau/GLIMPSE.git" -b master 
 
 set -Eeuo pipefail
 

test/simple_cromwell.conf

@@ -67,79 +67,5 @@ backend {
 
       }
     }
-
-    PAPIv2 {
-      actor-factory = "cromwell.backend.google.pipelines.v2beta.PipelinesApiLifecycleActorFactory"
-      config {
-        # Google project
-        project = "broad-dsde-methods"
-
-        # Base bucket for workflow executions
-        root = "gs://palantir-workflows-test-execution"
-
-        # Make the name of the backend used for call caching purposes insensitive to the PAPI version.
-        name-for-call-caching-purposes: PAPI
-
-        # Emit a warning if jobs last longer than this amount of time. This might indicate that something got stuck in PAPI.
-        slow-job-warning-time: 24 hours
-
-        genomics {
-          auth = "application-default"
-
-          # Endpoint for APIs, no reason to change this unless directed by Google.
-          endpoint-url = "https://lifesciences.googleapis.com/"
-
-          # Currently Cloud Life Sciences API is available only in `us-central1` and `europe-west2` locations.
-          location = "us-central1"
-
-          # Pipelines v2 only: specify the number of times localization and delocalization operations should be attempted
-          # There is no logic to determine if the error was transient or not, everything is retried upon failure
-          # Defaults to 3
-          localization-attempts = 3
-
-          # Specifies the minimum file size for `gsutil cp` to use parallel composite uploads during delocalization.
-          # Parallel composite uploads can result in a significant improvement in delocalization speed for large files
-          # but may introduce complexities in downloading such files from GCS, please see
-          # https://cloud.google.com/storage/docs/gsutil/commands/cp#parallel-composite-uploads for more information.
-          #
-          # If set to 0 parallel composite uploads are turned off. The default Cromwell configuration turns off
-          # parallel composite uploads, this sample configuration turns it on for files of 150M or larger.
-          parallel-composite-upload-threshold="150M"
-        }
-
-        filesystems {
-          gcs {
-            # A reference to a potentially different auth for manipulating files via engine functions.
-            auth = "application-default"
-            project = "broad-dsde-methods"
-
-            caching {
-              # When a cache hit is found, the following duplication strategy will be followed to use the cached outputs
-              # Possible values: "copy", "reference". Defaults to "copy"
-              # "copy": Copy the output files
-              # "reference": DO NOT copy the output files but point to the original output files instead.
-              #              Will still make sure than all the original output files exist and are accessible before
-              #              going forward with the cache hit.
-              duplication-strategy = "copy"
-            }
-          }
-        }
-
-        default-runtime-attributes {
-          cpu: 1
-          failOnStderr: false
-          continueOnReturnCode: 0
-          memory: "2048 MB"
-          bootDiskSizeGb: 10
-          # Allowed to be a String, or a list of Strings
-          disks: "local-disk 10 SSD"
-          noAddress: false
-          preemptible: 0
-          zones: ["us-central1-a", "us-central1-b"]
-        }
-
-        include "papi_v2_reference_image_manifest.conf"
-      }
-    }
   }
 }