Compile virion #1048
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| 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", "vroom", "magrittr", "fs", "data.table", "zip", "rglobi", "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@v2 | |
| with: | |
| name: GenBankFormatted | |
| path: Intermediate/Formatted/GenbankFormatted.csv.gz | |
| Globi: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - 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", "vroom", "magrittr", "fs", "data.table", "zip", "devtools", "lubridate", "here", "JuliaCall"), repos = "http://cran.us.r-project.org")' | |
| sudo Rscript -e 'devtools::install_github("ropensci/rglobi")' | |
| - 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: Download Globi | |
| run: | | |
| Rscript -e 'source("Code/02_3a_Download GLOBI.R")' | |
| - name: Digest Globi | |
| run: | | |
| Rscript -e 'source("Code/02_3b_Digest GLOBI.R")' | |
| - name: Format Globi | |
| run: | | |
| Rscript -e 'source("Code/02_3c_Format GLOBI.R")' | |
| - name: Save artifacts | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: GlobiFormatted | |
| path: Intermediate/Formatted/GLOBIFormatted.csv | |
| Finish: | |
| runs-on: ubuntu-latest | |
| needs: [GenBank, Globi] | |
| 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", "vroom", "magrittr", "fs", "data.table", "R.utils", "zip", "rglobi", "lubridate", "tidyft", "here", "JuliaCall"), repos = "http://cran.us.r-project.org")' | |
| - name: Get GenBank | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: GenBankFormatted | |
| - name: Get Globi | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: GlobiFormatted | |
| - 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@v2 | |
| 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. |