build.yml

name: CI

on:
  push:
    branches:
      - main
  pull_request:
    branches:
      - main

# cf. https://github.com/mamba-org/provision-with-micromamba#important
defaults:
  run:
    shell: bash -l {0}

env:
  MEHARI_VERSION: "0.25.4"

jobs:
  Build:
    strategy:
      matrix:
        genome_release:
          - grch37
          - grch38
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

      - name: Get current date
        id: date
        run: echo "::set-output name=date::$(date +'%Y-%m-%d')"

      - name: Cache data directory
        id: cache-primes
        uses: actions/cache@v3
        with:
          path: mehari-data-tx
          key: ${{ steps.date.outputs.date }}-${{ env.MEHARI_VERSION }}-${{ matrix.genome_release }}-${{ hashFiles('src/download.sh') }}

      - name: Install Conda environment
        uses: mamba-org/provision-with-micromamba@main
        with:
          environment-file: false
          environment-name: mehari-data-tx
          channels: conda-forge,bioconda,defaults
          extra-specs: |
            python =3.8
            entrez-direct =16.2
            biocommons.seqrepo =0.6.5
            htslib =1.17

      - name: Run the data build
        run: |
          export GENOME_RELEASE=${{ matrix.genome_release }}
          bash src/run.sh