Skip to content

Use gzip instead of pigz for kraken2 output compression #114

Use gzip instead of pigz for kraken2 output compression

Use gzip instead of pigz for kraken2 output compression #114

name: Build containers
on:
push:
branches:
- master
- develop
# Do the builds on all pull requests (to test them)
#pull_request: []
jobs:
build-test-containers:
runs-on: ubuntu-latest
strategy:
# Keep going on other deployments if anything bloops
fail-fast: false
matrix:
singularity_version:
- '3.8.1'
recipe:
- "workflow/envs/Singularity.biobakery"
- "workflow/envs/Singularity.krakenuniq"
- "workflow/envs/Singularity.snakemake"
- "workflow/envs/Singularity.stag-mwc"
container:
image: quay.io/singularity/singularity:v${{ matrix.singularity_version }}
options: --privileged
name: Check ${{ matrix.recipe }}
steps:
- name: Check out code for the container builds
uses: actions/checkout@v3
- name: Continue if Singularity Recipe exists
run: |
if [[ -f "${{ matrix.recipe }}" ]]; then
echo "keepgoing=true" >> $GITHUB_ENV
fi
- name: Build Container
if: ${{ env.keepgoing == 'true' }}
env:
recipe: ${{ matrix.recipe }}
run: |
ls
if [ -f "${{ matrix.recipe }}" ]; then
sudo -E singularity build container.sif ${{ matrix.recipe }}
tag=$(basename "${recipe/Singularity\./}-${GITHUB_REF_NAME}")
# Build the container and name by tag
echo "Tag is $tag."
echo "tag=$tag" >> $GITHUB_ENV
else
echo "${{ matrix.recipe }} is not found."
echo "Present working directory: $PWD"
ls
fi
- name: Login and Deploy Container
if: (github.event_name != 'pull_request')
env:
keepgoing: ${{ env.keepgoing }}
run: |
if [[ "${keepgoing}" == "true" ]]; then
echo ${{ secrets.GITHUB_TOKEN }} | singularity remote login -u ${{ secrets.GHCR_USERNAME }} --password-stdin oras://ghcr.io
singularity push container.sif oras://ghcr.io/${GITHUB_REPOSITORY}:${tag}
fi