Compile virion #1177
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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. |