-
Notifications
You must be signed in to change notification settings - Fork 2
59 lines (47 loc) · 1.19 KB
/
apptainer.yml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
name: Apptainer Run
on:
push:
branches:
- main
- dev
workflow_dispatch:
pull_request:
branches-ignore: []
schedule:
- cron: '0 0 20 * *'
jobs:
build-linux:
runs-on: ubuntu-latest
strategy:
max-parallel: 5
matrix:
python: [3.8, '3.10']
fail-fast: false
steps:
- name: precleanup
run: |
sudo rm -rf /usr/share/dotnet
sudo rm -rf "$AGENT_TOOLSDIRECTORY"
- name: install graphviz
run: |
sudo apt update
sudo apt-get install -y graphviz software-properties-common
sudo add-apt-repository -y ppa:apptainer/ppa
sudo apt update
sudo apt install -y apptainer
- name: checkout git repo
uses: actions/checkout@v3
- name: Set up Python 3.X
uses: actions/setup-python@v3
with:
python-version: ${{ matrix.python }}
- name: Install dependencies
run: |
pip install .[testing]
- name: install package itself
run: |
pip install .
pip install "pulp==2.7.0" --no-deps
- name: testing
run: |
sequana_denovo --input-directory test/data/ --use-apptainer && cd denovo && sh denovo.sh