From ecc853d573e2309bb5ca9f63c76ae0c4e2bddda8 Mon Sep 17 00:00:00 2001 From: Adam Nichols Date: Tue, 18 Jul 2023 15:55:55 -0400 Subject: [PATCH 1/4] DRS image build updates --- project/Settings.scala | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/project/Settings.scala b/project/Settings.scala index 0257cbac06b..065615aeb8f 100644 --- a/project/Settings.scala +++ b/project/Settings.scala @@ -127,12 +127,13 @@ object Settings { */ val installLocalizerSettings: List[Setting[Seq[Instruction]]] = List( dockerCustomSettings := List( + Instructions.From("ubuntu:latest"), Instructions.Env("PATH", "$PATH:/usr/local/gcloud/google-cloud-sdk/bin"), // instructions to install `crcmod` Instructions.Run("apt-get -y update"), Instructions.Run("apt-get -y install python3.11"), - Instructions.Run("apt -y install python3-pip"), - Instructions.Run("apt-get -y install gcc python3-dev python3-setuptools"), + Instructions.Run("apt-get -y install python3-pip"), + Instructions.Run("apt-get -y install curl gcc python3-dev python3-setuptools"), Instructions.Run("pip3 uninstall crcmod"), Instructions.Run("pip3 install --no-cache-dir -U crcmod"), Instructions.Run("update-alternatives --install /usr/bin/python python /usr/bin/python3 1"), From 344e3a47a16845121927e823b0f15a6fbffa3b7e Mon Sep 17 00:00:00 2001 From: Adam Nichols Date: Wed, 19 Jul 2023 10:29:42 -0400 Subject: [PATCH 2/4] Specific image for failing test --- .../resources/standardTestCases/drs_tests/drs_usa_jdr.wdl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/centaur/src/main/resources/standardTestCases/drs_tests/drs_usa_jdr.wdl b/centaur/src/main/resources/standardTestCases/drs_tests/drs_usa_jdr.wdl index ba2a17f292d..e9b56af98d2 100644 --- a/centaur/src/main/resources/standardTestCases/drs_tests/drs_usa_jdr.wdl +++ b/centaur/src/main/resources/standardTestCases/drs_tests/drs_usa_jdr.wdl @@ -61,7 +61,7 @@ task localize_jdr_drs_with_usa { } runtime { - docker: "ubuntu" + docker: "ubuntu:latest" backend: "papi-v2-usa" } } @@ -88,7 +88,7 @@ task skip_localize_jdr_drs_with_usa { } runtime { - docker: "ubuntu" + docker: "ubuntu:latest" backend: "papi-v2-usa" } } @@ -109,7 +109,7 @@ task read_drs_with_usa { } runtime { - docker: "ubuntu" + docker: "ubuntu:latest" backend: "papi-v2-usa" } } From ebe7c13a323a19148668292663a942cc08ccdf6f Mon Sep 17 00:00:00 2001 From: Adam Nichols Date: Wed, 19 Jul 2023 10:47:06 -0400 Subject: [PATCH 3/4] Remove GitHub Actions `self-hosted` --- .github/workflows/chart_update_on_merge.yml | 2 +- .github/workflows/docker_build_test.yml | 2 +- .github/workflows/make_publish_prs.yml | 3 +-- 3 files changed, 3 insertions(+), 4 deletions(-) diff --git a/.github/workflows/chart_update_on_merge.yml b/.github/workflows/chart_update_on_merge.yml index 107e9d5de4a..a31a5c24ed3 100644 --- a/.github/workflows/chart_update_on_merge.yml +++ b/.github/workflows/chart_update_on_merge.yml @@ -9,7 +9,7 @@ jobs: chart-update: name: Cromwhelm Chart Auto Updater if: github.event.pull_request.merged == true - runs-on: self-hosted # Faster machines; see https://github.com/broadinstitute/cromwell/settings/actions/runners + runs-on: ubuntu-latest steps: - name: Clone Cromwell uses: actions/checkout@v2 diff --git a/.github/workflows/docker_build_test.yml b/.github/workflows/docker_build_test.yml index 15517cce919..01c2ea502c9 100644 --- a/.github/workflows/docker_build_test.yml +++ b/.github/workflows/docker_build_test.yml @@ -17,7 +17,7 @@ permissions: jobs: sbt-build: name: sbt docker build - runs-on: self-hosted + runs-on: ubuntu-latest steps: - name: Clone Cromwell uses: actions/checkout@v2 diff --git a/.github/workflows/make_publish_prs.yml b/.github/workflows/make_publish_prs.yml index 4a25210dd6e..e4e98a7f2f0 100644 --- a/.github/workflows/make_publish_prs.yml +++ b/.github/workflows/make_publish_prs.yml @@ -16,7 +16,7 @@ on: jobs: make-firecloud-develop-pr: name: Create firecloud-develop PR - runs-on: self-hosted # Faster machines; see https://github.com/broadinstitute/cromwell/settings/actions/runners + runs-on: ubuntu-latest steps: - name: Clone firecloud-develop uses: actions/checkout@v2 @@ -70,4 +70,3 @@ jobs: 'It updates cromwell from version ${{ github.event.inputs.old_cromwell_version }} to ${{ github.event.inputs.new_cromwell_version }}.' ].join('\n') }); - From 1437fe91a1c9598ee4b6a49f2e8d776185eea01e Mon Sep 17 00:00:00 2001 From: Adam Nichols Date: Wed, 19 Jul 2023 16:31:21 -0400 Subject: [PATCH 4/4] `wget` seems more stable in terms of not getting SSL errors `From` is not necessary because we found the place we specify "Debian" a.k.a. Ubuntu --- project/Settings.scala | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/project/Settings.scala b/project/Settings.scala index 065615aeb8f..ea775ed2bf5 100644 --- a/project/Settings.scala +++ b/project/Settings.scala @@ -127,19 +127,18 @@ object Settings { */ val installLocalizerSettings: List[Setting[Seq[Instruction]]] = List( dockerCustomSettings := List( - Instructions.From("ubuntu:latest"), Instructions.Env("PATH", "$PATH:/usr/local/gcloud/google-cloud-sdk/bin"), // instructions to install `crcmod` Instructions.Run("apt-get -y update"), Instructions.Run("apt-get -y install python3.11"), Instructions.Run("apt-get -y install python3-pip"), - Instructions.Run("apt-get -y install curl gcc python3-dev python3-setuptools"), + Instructions.Run("apt-get -y install wget gcc python3-dev python3-setuptools"), Instructions.Run("pip3 uninstall crcmod"), Instructions.Run("pip3 install --no-cache-dir -U crcmod"), Instructions.Run("update-alternatives --install /usr/bin/python python /usr/bin/python3 1"), Instructions.Env("CLOUDSDK_PYTHON", "python3"), // instructions to install Google Cloud SDK - Instructions.Run("curl https://dl.google.com/dl/cloudsdk/release/google-cloud-sdk.tar.gz > /tmp/google-cloud-sdk.tar.gz"), + Instructions.Run("wget https://dl.google.com/dl/cloudsdk/release/google-cloud-sdk.tar.gz -O /tmp/google-cloud-sdk.tar.gz"), Instructions.Run("""mkdir -p /usr/local/gcloud \ | && tar -C /usr/local/gcloud -xvf /tmp/google-cloud-sdk.tar.gz \ | && /usr/local/gcloud/google-cloud-sdk/install.sh""".stripMargin),