Create all entities in Seqera Platform from end-to-end with seqerakit #75
Workflow file for this run
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name: e2e-testing | |
run-name: Create all entities in Seqera Platform from end-to-end with seqerakit | |
# This workflow can be triggered manually with GitHub actions workflow dispatch button. | |
# It will automate the end-to-end creation all of the following entities in Seqera Platform. | |
on: | |
pull_request_target: | |
branches: [main] | |
workflow_dispatch: | |
inputs: | |
pre_delete: | |
description: 'Delete all entities in the yaml before testing' | |
required: false | |
type: boolean | |
default: false | |
clearup: | |
description: 'Clearup all entities in yaml after testing' | |
required: false | |
type: boolean | |
default: true | |
jobs: | |
e2e-testing: | |
name: | |
if: github.repository == 'seqeralabs/seqera-kit' | |
runs-on: ubuntu-latest | |
defaults: | |
run: | |
shell: bash -el {0} | |
env: | |
TOWER_ACCESS_TOKEN: ${{ secrets.TOWER_ACCESS_TOKEN }} | |
TOWER_GITHUB_PASSWORD: ${{ secrets.TOWER_GITHUB_PASSWORD }} | |
DOCKERHUB_PASSWORD: ${{ secrets.DOCKERHUB_PASSWORD }} | |
AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
AWS_ASSUME_ROLE_ARN: ${{ secrets.AWS_ASSUME_ROLE_ARN }} | |
AZURE_BATCH_KEY: ${{ secrets.AZURE_BATCH_KEY }} | |
AZURE_STORAGE_KEY: ${{ secrets.AZURE_STORAGE_KEY }} | |
GOOGLE_KEY: ${{ secrets.GOOGLE_KEY }} | |
SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }} | |
steps: | |
- name: Check out source-code repository | |
uses: actions/checkout@v3 | |
- name: Setup conda | |
uses: conda-incubator/setup-miniconda@v3 | |
with: | |
auto-update-conda: true | |
environment-file: environment.yml | |
python-version: '3.12' | |
mamba-version: '*' | |
channels: conda-forge,bioconda,defaults | |
activate-environment: seqerakit | |
use-mamba: true | |
- name: Install Tower CLI v0.9.1 | |
run: | | |
wget https://github.com/seqeralabs/tower-cli/releases/download/v0.9.1/tw-linux-x86_64 \ | |
&& chmod +x tw-linux-x86_64 \ | |
&& sudo mv tw-linux-x86_64 /usr/local/bin/tw | |
- name: Install pip & seqerakit | |
run: | | |
pip install -e . | |
- name: pre-clear | |
# Note this task always 'succeeds' | |
if: ( success() || failure() ) && ( github.event_name != 'workflow_dispatch' || inputs.pre_delete ) | |
run: | | |
mamba init | |
temp_file=$(mktemp -q) | |
echo $GOOGLE_KEY | base64 -d > $temp_file | |
export GOOGLE_KEY=$temp_file | |
seqerakit examples/yaml/e2e/*.yml --delete || true | |
- name: dryrun | |
run: | | |
mamba init | |
temp_file=$(mktemp -q) | |
echo $GOOGLE_KEY | base64 -d > $temp_file | |
export GOOGLE_KEY=$temp_file | |
seqerakit examples/yaml/e2e/*.yml --dryrun | |
- name: create | |
run: | | |
mamba init | |
temp_file=$(mktemp -q) | |
echo $GOOGLE_KEY | base64 -d > $temp_file | |
export GOOGLE_KEY=$temp_file | |
seqerakit examples/yaml/e2e/*.yml | |
- name: teardown | |
if: ( success() || failure() ) && ( github.event_name != 'workflow_dispatch' || inputs.clearup ) | |
run: | | |
mamba init | |
temp_file=$(mktemp -q) | |
echo $GOOGLE_KEY | base64 -d > $temp_file | |
export GOOGLE_KEY=$temp_file | |
seqerakit examples/yaml/e2e/*.yml --delete |