-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Add CI/CD for using dockerfile for wdl
- Loading branch information
Showing
1 changed file
with
39 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,39 @@ | ||
name: MiniWDL linter CI Dev DockerFile | ||
|
||
on: | ||
push: | ||
workflow_dispatch: | ||
|
||
jobs: | ||
run-miniwdl: | ||
runs-on: ubuntu-latest | ||
|
||
steps: | ||
- name: Checkout repository | ||
uses: actions/checkout@v2 | ||
|
||
- name: Set up Python | ||
uses: actions/setup-python@v2 | ||
with: | ||
python-version: '3.8' # specify the Python version you need | ||
|
||
- name: Install Docker | ||
run: | | ||
sudo apt-get update | ||
sudo apt-get install -y docker.io | ||
sudo systemctl start docker | ||
sudo systemctl enable docker | ||
sudo usermod -aG docker $USER | ||
- name: Build Docker Image | ||
run: | | ||
docker build -t local-metams:latest . | ||
- name: Install MiniWDL | ||
run: | | ||
python -m pip install --upgrade pip | ||
pip install miniwdl | ||
- name: Run MiniWDL | ||
run: | | ||
miniwdl run wdl/metaMS_lipidomics.wdl -i wdl/metams_input_lipidomics.json --verbose --no-cache --copy-input-files |