-
Notifications
You must be signed in to change notification settings - Fork 6
67 lines (57 loc) · 1.99 KB
/
ci.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
58
59
60
61
62
63
64
65
66
67
name: Unit tests
on: [push, pull_request]
env:
MONGODB_VERSION: 3.6.14
MINICONDA_VERSION: "4.10.3"
CONDA_GENERIC_CHANNEL: "https://dnap.cog.sanger.ac.uk/npg/conda/prod/generic/linux-64/"
CONDA_GENERIC_DEVEL_CHANNEL: "https://dnap.cog.sanger.ac.uk/npg/conda/devel/generic/linux-64/"
MINICONDA_HOME: "/tmp/miniconda"
SOFTWARE_HOME: "/tmp/software"
FREEBAYES_VERSION: "1.2.0"
BIOBAMBAM_VERSION: "2.0.79"
SAMTOOLS1_VERSION: "1.14.0"
jobs:
test:
strategy:
fail-fast: false
matrix:
os: [ubuntu-latest]
node-version: ["12.14.1", "14", "16"]
runs-on: ${{ matrix.os }}
steps:
- name: Check out repository code
uses: actions/checkout@v3
- uses: actions/setup-node@v3
with:
node-version: ${{ matrix.node-version }}
- name: Cache node modules
uses: actions/cache@v3
env:
cache-name: cache-node-modules
with:
path: ~/.npm
key: ${{ runner.os }}-build-${{ env.cache-name }}-${{ hashFiles('**/package-lock.json') }}
restore-keys: |
${{ runner.os }}-build-${{ env.cache-name }}-
- name: Cache conda modules
uses: actions/cache@v3
env:
cache-name: cache-conda-modules
with:
path: /tmp/software
key: ${{ runner.os }}-build-${{ env.cache-name }}-${{env.MONGODB_VERSION}}-${{env.MINICONDA_VERSION}}-${{env.FREEBAYES_VERSION}}-${{env.BIOBAMBAM_VERSION}}-${{env.SAMTOOLS1_VERSION}}
restore-keys: |
${{ runner.os }}-build-${{ env.cache-name }}-${{env.MONGODB_VERSION}}-${{env.MINICONDA_VERSION}}-${{env.FREEBAYES_VERSION}}-${{env.BIOBAMBAM_VERSION}}-${{env.SAMTOOLS1_VERSION}}
- name: Setup dependencies
run: |
./scripts/CI-install.sh
export PATH="/tmp/usr/bin:${PATH}"
npm install
npm install -g grunt-cli
npm --version
mongo --version
conda --version
bamstreamingmarkduplicates --version
samtools --version
- name: Run tests
run: grunt -v