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Fix trial rebuilds #239

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merged 2 commits into from
Feb 16, 2024
Merged

Fix trial rebuilds #239

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f4c292c
Fix trial builds for rebuild workflows
joverlee521 Feb 15, 2024
85e3364
rebuilds: Use TEST_SLACK_CHANNEL for trial builds
joverlee521 Feb 15, 2024
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31 changes: 24 additions & 7 deletions .github/workflows/rebuild-hmpxv1-big.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,18 +9,34 @@ on:
workflow_dispatch:
inputs:
trial_name:
description: "If set, result will be at nextstrain.org/staging/trial/trial_name/mpox/mpxv"
description: "If set, result will be at nextstrain.org/staging/trial/${trial_name}/${auspice_name}"
required: false
image:
description: 'Specific container image to use for build (will override the default of "nextstrain build")'
required: false

env:
TRIAL_NAME: ${{ github.event.inputs.trial_name }}
NEXTSTRAIN_DOCKER_IMAGE: ${{ github.event.inputs.image }}

jobs:
set_config_overrides:
runs-on: ubuntu-latest
steps:
- id: config
name: Set config overrides
env:
TRIAL_NAME: ${{ inputs.trial_name }}
run: |
config=""
if [[ "$TRIAL_NAME" ]]; then
config+="--config"
config+=" deploy_url='s3://nextstrain-staging/'"
config+=" auspice_prefix='"$TRIAL_NAME"'"
fi

echo "config=$config" >> "$GITHUB_OUTPUT"
outputs:
config_overrides: ${{ steps.config.outputs.config }}

rebuild_hmpxv1_big:
needs: [set_config_overrides]
permissions:
id-token: write
uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
Expand All @@ -29,8 +45,9 @@ jobs:
runtime: aws-batch
env: |
NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.image }}
CONFIG_OVERRIDES: ${{ needs.set_config_overrides.outputs.config_overrides }}
GITHUB_RUN_ID: ${{ github.run_id }}
SLACK_CHANNELS: ${{ vars.SLACK_CHANNELS }}
SLACK_CHANNELS: ${{ inputs.trial_name && vars.TEST_SLACK_CHANNEL || vars.SLACK_CHANNELS }}
BUILD_DIR: phylogenetic
BUILD_NAME: hmpxv1_big
run: |
Expand All @@ -47,4 +64,4 @@ jobs:
. \
notify_on_deploy \
--configfiles $BUILD_DIR/config/$BUILD_NAME/config.yaml $BUILD_DIR/config/nextstrain_automation.yaml \
--config auspice_prefix=$TRIAL_NAME --directory $BUILD_DIR --snakefile $BUILD_DIR/Snakefile
$CONFIG_OVERRIDES --directory $BUILD_DIR --snakefile $BUILD_DIR/Snakefile
31 changes: 24 additions & 7 deletions .github/workflows/rebuild-hmpxv1.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,18 +9,34 @@ on:
workflow_dispatch:
inputs:
trial_name:
description: "If set, result will be at nextstrain.org/staging/trial/trial_name/mpox/mpxv"
description: "If set, result will be at nextstrain.org/staging/trial/${trial_name}/${auspice_name}"
required: false
image:
description: 'Specific container image to use for build (will override the default of "nextstrain build")'
required: false

env:
TRIAL_NAME: ${{ github.event.inputs.trial_name }}
NEXTSTRAIN_DOCKER_IMAGE: ${{ github.event.inputs.image }}

jobs:
set_config_overrides:
runs-on: ubuntu-latest
steps:
- id: config
name: Set config overrides
env:
TRIAL_NAME: ${{ inputs.trial_name }}
run: |
config=""
if [[ "$TRIAL_NAME" ]]; then
config+="--config"
config+=" deploy_url='s3://nextstrain-staging/'"
config+=" auspice_prefix='"$TRIAL_NAME"'"
fi

echo "config=$config" >> "$GITHUB_OUTPUT"
outputs:
config_overrides: ${{ steps.config.outputs.config }}

rebuild_hmpxv1:
needs: [set_config_overrides]
permissions:
id-token: write
uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
Expand All @@ -29,8 +45,9 @@ jobs:
runtime: aws-batch
env: |
NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.image }}
CONFIG_OVERRIDES: ${{ needs.set_config_overrides.outputs.config_overrides }}
GITHUB_RUN_ID: ${{ github.run_id }}
SLACK_CHANNELS: ${{ vars.SLACK_CHANNELS }}
SLACK_CHANNELS: ${{ inputs.trial_name && vars.TEST_SLACK_CHANNEL || vars.SLACK_CHANNELS }}
BUILD_DIR: phylogenetic
BUILD_NAME: hmpxv1
run: |
Expand All @@ -47,4 +64,4 @@ jobs:
. \
notify_on_deploy \
--configfiles $BUILD_DIR/config/$BUILD_NAME/config.yaml $BUILD_DIR/config/nextstrain_automation.yaml \
--config auspice_prefix=$TRIAL_NAME --directory $BUILD_DIR --snakefile $BUILD_DIR/Snakefile
$CONFIG_OVERRIDES --directory $BUILD_DIR --snakefile $BUILD_DIR/Snakefile
31 changes: 24 additions & 7 deletions .github/workflows/rebuild-mpxv.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,18 +9,34 @@ on:
workflow_dispatch:
inputs:
trial_name:
description: "If set, result will be at nextstrain.org/staging/trial/trial_name/mpox/mpxv"
description: "If set, result will be at nextstrain.org/staging/trial/${trial_name}/${auspice_name}"
required: false
image:
description: 'Specific container image to use for build (will override the default of "nextstrain build")'
required: false

env:
TRIAL_NAME: ${{ github.event.inputs.trial_name }}
NEXTSTRAIN_DOCKER_IMAGE: ${{ github.event.inputs.image }}

jobs:
set_config_overrides:
runs-on: ubuntu-latest
steps:
- id: config
name: Set config overrides
env:
TRIAL_NAME: ${{ inputs.trial_name }}
run: |
config=""
if [[ "$TRIAL_NAME" ]]; then
config+="--config"
config+=" deploy_url='s3://nextstrain-staging/'"
config+=" auspice_prefix='"$TRIAL_NAME"'"
fi

echo "config=$config" >> "$GITHUB_OUTPUT"
outputs:
config_overrides: ${{ steps.config.outputs.config }}

rebuild_mpxv:
needs: [set_config_overrides]
permissions:
id-token: write
uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
Expand All @@ -29,8 +45,9 @@ jobs:
runtime: aws-batch
env: |
NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.image }}
CONFIG_OVERRIDES: ${{ needs.set_config_overrides.outputs.config_overrides }}
GITHUB_RUN_ID: ${{ github.run_id }}
SLACK_CHANNELS: ${{ vars.SLACK_CHANNELS }}
SLACK_CHANNELS: ${{ inputs.trial_name && vars.TEST_SLACK_CHANNEL || vars.SLACK_CHANNELS }}
BUILD_DIR: phylogenetic
BUILD_NAME: mpxv
run: |
Expand All @@ -47,4 +64,4 @@ jobs:
. \
notify_on_deploy \
--configfiles $BUILD_DIR/config/$BUILD_NAME/config.yaml $BUILD_DIR/config/nextstrain_automation.yaml \
--config auspice_prefix=$TRIAL_NAME --directory $BUILD_DIR --snakefile $BUILD_DIR/Snakefile
$CONFIG_OVERRIDES --directory $BUILD_DIR --snakefile $BUILD_DIR/Snakefile
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