Skip to content

Nightly Uploader

Nightly Uploader #17

Workflow file for this run

name: Nightly Uploader
on:
schedule:
- cron: '12 2 * * *'
jobs:
build-linux:
name: Linux Upload
if: github.repository == 'bioconda/bioconda-recipes'
runs-on: ubuntu-latest
strategy:
fail-fast: false
max-parallel: 13
steps:
- uses: actions/checkout@v3
with:
fetch-depth: 0
- name: set path
run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
- name: Fetch conda install script
run: |
wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh
- name: Restore cache
id: cache
uses: actions/cache@v3
with:
path: /opt/mambaforge
key: ${{ runner.os }}--bulk--${{ hashFiles('**/install-and-set-up-conda.sh') }}
- name: Set up bioconda-utils
if: steps.cache.outputs.cache-hit != 'true'
run: bash install-and-set-up-conda.sh
# This script can be used to 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 with --system).
- name: Configure conda
run: bash configure-conda.sh
- name: Build and upload
env:
QUAY_LOGIN: ${{ secrets.QUAY_LOGIN }}
QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }}
ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
INVOLUCRO_AUTH: ${{ secrets.INVOLUCRO_AUTH }}
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
# Mimic circleci
OSTYPE: "linux-gnu"
CI: "true"
run: |
set -ex
eval "$(conda shell.bash hook)"
conda activate bioconda
docker pull quay.io/dpryan79/mulled_container:latest
bioconda-utils build recipes config.yml \
--docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers \
--prelint
docker rmi quay.io/dpryan79/mulled_container:latest
build-osx:
name: OSX Tests
if: github.repository == 'bioconda/bioconda-recipes'
runs-on: macOS-latest
strategy:
fail-fast: false
max-parallel: 4
steps:
- uses: actions/checkout@v3
with:
fetch-depth: 0
- name: set path
run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
- name: Fetch conda install script
run: |
wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh
- name: Restore cache
id: cache
uses: actions/cache@v3
with:
path: /opt/mambaforge
key: ${{ runner.os }}--bulk--${{ hashFiles('**/install-and-set-up-conda.sh') }}
- name: Set up bioconda-utils
if: steps.cache.outputs.cache-hit != 'true'
run: bash install-and-set-up-conda.sh
# This script can be used to 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 with --system).
- name: Configure conda
run: bash configure-conda.sh
- name: Build and Test
env:
QUAY_LOGIN: ${{ secrets.QUAY_LOGIN }}
QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }}
ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
INVOLUCRO_AUTH: ${{ secrets.INVOLUCRO_AUTH }}
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
# Mimic circleci
OSTYPE: "darwin"
CI: "true"
run: |
set -e
eval "$(conda shell.bash hook)"
conda activate bioconda
# The SDK isn't actually cached, so reinstall it
run_conda_forge_build_setup
bioconda-utils build recipes config.yml \
--anaconda-upload \
--prelint