main.yml

name: Compile virion

# Controls when the action will run.
on:
  push:
    branches:
      - main
  pull_request:
    branches:
      - main
  # run once a week
  schedule:
    - cron: "0 0 * * *"
  workflow_dispatch:
jobs:
  GenBank:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v3
    - uses: gautamkrishnar/keepalive-workflow@v1
    - name: Setup Julia
      uses: julia-actions/setup-julia@v1
      with:
        version: 1.7
    - name: Julia dependencies (DF)
      run: julia -e 'using Pkg; Pkg.activate("."); Pkg.add("CSV"); Pkg.add("DataFrames")'
    - name: NCBITaxonomy (version from MAIN branch!)
      run: julia -e 'using Pkg; Pkg.activate("."); Pkg.add(PackageSpec(name="NCBITaxonomy", rev="main"))'
    - name: Setup R
      uses: r-lib/actions/setup-r@v2
    - name: Libraries for tidyverse
      run: sudo apt-get install -y libharfbuzz-dev libfribidi-dev
    - name: dependencies!!!!
      run: |
        sudo apt-get install libcurl4-openssl-dev libarchive-dev
        sudo Rscript -e 'install.packages(c("taxize", "tidyverse", "RCurl", "readr", "rentrez", "vroom", "magrittr", "fs", "data.table", "zip", "lubridate", "R.utils", "here", "JuliaCall"), repos = "http://cran.us.r-project.org")'
    - name: Download GenBank
      run: |
        Rscript -e 'source("Code/02_1a_Download GenBank.R")'
    - name: Digest GenBank
      run: |
        Rscript -e 'source("Code/02_1b_Digest GenBank.R")'
    - name: Format GenBank
      run: |
        Rscript -e 'source("Code/02_1c_Format GenBank.R")'
    - name: Save artifacts
      uses: actions/upload-artifact@v4
      with:
        name: GenBankFormatted
        path: Intermediate/Formatted/GenbankFormatted.csv.gz
  Finish:
    runs-on: ubuntu-latest
    needs: [GenBank]
    steps:
    - uses: actions/checkout@v3
    - name: Setup R
      uses: r-lib/actions/setup-r@v2
    - name: dependencies!!!
      run: |
        sudo apt-get install libcurl4-openssl-dev libarchive-dev libharfbuzz-dev libfribidi-dev
        sudo Rscript -e 'install.packages(c("taxize", "tidyverse", "RCurl", "readr", "rentrez", "vroom", "magrittr", "fs", "data.table", "R.utils", "zip", "lubridate", "tidyft", "here", "JuliaCall"), repos = "http://cran.us.r-project.org")'
    - name: Get GenBank
      uses: actions/download-artifact@v4
      with:
        name: GenBankFormatted
    - name: Merge clean files
      run: |
        Rscript -e 'source("Code/03_Merge clean files.R")'
    - name: High level checks
      run: |
        Rscript -e 'source("Code/04_High level VIRION checks.R")'
    - name: Dissolve VIRION
      run: |
        Rscript -e 'source("Code/05_Dissolve VIRION.R")'
    - name: Save the artifacts
      uses: actions/upload-artifact@v4
      with:
        name: VIRION
        path: Virion
    - name: Deploy
      uses: JamesIves/github-pages-deploy-action@4.1.7
      with:
        branch: gh-pages # The branch the action should deploy to.
        folder: Virion # The folder the action should deploy.