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fix handling of dominant / recessive #98

fix handling of dominant / recessive

fix handling of dominant / recessive #98

name: build development images
on:
push:
branches:
- dev
env:
REGISTRY_USERNAME: ${{ secrets.DOCKER_USERNAME }}
REGISTRY_TOKEN: ${{ secrets.DOCKER_TOKEN }}
DOCKER_REGISTRY_LOGIN: "dockerhub.ebi.ac.uk"
SINGULARITY_REGISTRY_LOGIN: "oras://dockerhub.ebi.ac.uk"
DOCKER_REGISTRY: "dockerhub.ebi.ac.uk/gdp-public/pgscatalog_utils"
SINGULARITY_REGISTRY: "oras://dockerhub.ebi.ac.uk/gdp-public/pgscatalog_utils/singularity"
SINGULARITY_VERSION: "3.8.3"
jobs:
build_docker_dev:
name: build docker development image
runs-on: ubuntu-latest
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
- name: Set up QEMU
uses: docker/setup-qemu-action@v2
with:
platforms: arm64
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
- name: Login to Docker Hub
uses: docker/login-action@v2
with:
registry: ${{ env.DOCKER_REGISTRY_LOGIN }}
username: ${{ env.REGISTRY_USERNAME }}
password: ${{ env.REGISTRY_TOKEN }}
- name: Build and push
uses: docker/build-push-action@v3
with:
push: true
platforms: "linux/amd64,linux/arm64"
tags: ${{ env.DOCKER_REGISTRY }}/pgscatalog_utils:dev
build_singularity_dev:
needs: build_docker_dev
name: build singularity development image
runs-on: ubuntu-latest
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
- name: Cache singularity setup
id: cache-singularity
uses: actions/cache@v3
with:
path: /opt/hostedtoolcache/singularity/${{ env.SINGULARITY_VERSION }}/x64
key: ${{ runner.os }}-singularity-${{ env.SINGULARITY_VERSION }}
- name: Set up Singularity
uses: eWaterCycle/setup-singularity@v7
if: steps.cache-singularity.outputs.cache-hit != 'true'
with:
singularity-version: ${{ env.SINGULARITY_VERSION }}
- name: Add singularity to path
if: steps.cache-singularity.outputs.cache-hit == 'true'
run: |
echo "/opt/hostedtoolcache/singularity/${{ env.SINGULARITY_VERSION }}/x64/bin" >> $GITHUB_PATH
- name: Build singularity image
run: singularity build img.sif "docker://${DOCKER_REGISTRY}/pgscatalog_utils:dev"
- name: Push singularity image
run: |
echo "$REGISTRY_TOKEN" | singularity remote login -u "$REGISTRY_USERNAME" --password-stdin "$SINGULARITY_REGISTRY_LOGIN"
singularity push img.sif "${SINGULARITY_REGISTRY}/pgscatalog_utils:dev"