/
azure-pipeline-nightly.yml
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/
azure-pipeline-nightly.yml
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schedules:
- cron: "0 0 * * *"
displayName: Nightly uploader
branches:
include:
- master
always: true
pr: none
trigger:
branches:
exclude:
- "*"
jobs:
- job: "build_and_push_linux"
pool:
vmImage: "ubuntu-latest"
strategy:
maxParallel: 8
timeoutInMinutes: 360
steps:
- script: |
git checkout master
- bash: echo "##vso[task.prependpath]/opt/mambaforge/bin"
displayName: Add conda to PATH
- bash: |
wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{common,install-and-set-up-conda,configure-conda}.sh
displayName: Fetch bioconda install script
- bash: |
sudo mkdir -p /opt
sudo chown -R $USER /opt
displayName: Ensure cache has path to restore to
- task: Cache@2
inputs:
path: "/opt/mambaforge"
key: '"$(Agent.OS)" | install-and-set-up-conda.sh | configure-conda.sh | common.sh'
cacheHitVar: CACHE_RESTORED
displayName: Restore cache
- script: bash install-and-set-up-conda.sh
condition: ne(variables.CACHE_RESTORED, 'true')
displayName: Install bioconda-utils
# We reconfigure conda to use the right channel setup.
# This has to be done after the cache is restored, because
# the channel setup is not cached as it resides in the home directory.
# We could use a system-wide (and therefore cached) channel setup,
# but mamba does not support that at the time of implementation
# (it ignores settings made by --system).
- script: bash configure-conda.sh
displayName: Configure conda
- bash: |
set -e
eval "$(conda shell.bash hook)"
conda activate bioconda
conda build --token $ANACONDA_TOKEN --user bioconda --quiet recipes/bioconda-repodata-patches
env:
ANACONDA_TOKEN: $(ANACONDA_TOKEN)
displayName: Rebuild and push the bioconda-repodata-patches package
- bash: |
set -e
eval "$(conda shell.bash hook)"
conda activate bioconda
docker pull quay.io/dpryan79/mulled_container:latest
export OSTYPE="linux-gnu"
export CI="true"
# build and push all leftover packages
bioconda-utils build recipes config.yml \
--docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers \
--prelint --exclude bioconda-repodata-patches
docker rmi quay.io/dpryan79/mulled_container:latest
env:
QUAY_OAUTH_TOKEN: $(QUAY_OAUTH_TOKEN)
ANACONDA_TOKEN: $(ANACONDA_TOKEN)
INVOLUCRO_AUTH: $(INVOLUCRO_AUTH)
displayName: Build and push leftover packages
- job: "build_and_push_osx"
pool:
vmImage: "macOS-latest"
strategy:
maxParallel: 4
timeoutInMinutes: 360
steps:
- script: |
git checkout master
- bash: echo "##vso[task.prependpath]/opt/mambaforge/bin"
displayName: Add conda to PATH
- bash: |
wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{common,install-and-set-up-conda,configure-conda}.sh
displayName: Fetch bioconda install script
- bash: |
sudo mkdir -p /opt
sudo chown -R $USER /opt
displayName: Ensure cache has path to restore to
- task: Cache@2
inputs:
path: "/opt/mambaforge"
key: '"$(Agent.OS)" | install-and-set-up-conda.sh | configure-conda.sh | common.sh'
cacheHitVar: CACHE_RESTORED
displayName: Restore cache
- script: bash install-and-set-up-conda.sh
condition: ne(variables.CACHE_RESTORED, 'true')
displayName: Install bioconda-utils
# We reconfigure conda to use the right channel setup.
# This has to be done after the cache is restored, because
# the channel setup is not cached as it resides in the home directory.
# We could use a system-wide (and therefore cached) channel setup,
# but mamba does not support that at the time of implementation
# (it ignores settings made by --system).
- script: bash configure-conda.sh
displayName: Configure conda
- bash: |
set -e
eval "$(conda shell.bash hook)"
conda activate bioconda
export OSTYPE="darwin"
export CI="true"
bioconda-utils build recipes config.yml \
--anaconda-upload \
--prelint
env:
QUAY_OAUTH_TOKEN: $(QUAY_OAUTH_TOKEN)
ANACONDA_TOKEN: $(ANACONDA_TOKEN)
INVOLUCRO_AUTH: $(INVOLUCRO_AUTH)
displayName: Build and push leftover packages