Merge branch 'main' into branch_name

.github/workflows/main.yml

@@ -8,67 +8,38 @@ on:
   pull_request:
     branches:
       - main
-  # run once a week
+  # run once a week 
   schedule:
     - cron: "0 0 * * *"
-  workflow_dispatch:
+  workflow_dispatch: 
 jobs:
   GenBank:
     runs-on: ubuntu-latest
+    container: colebrookson/virion:latest   
     steps:
     - uses: actions/checkout@v3
-    - uses: gautamkrishnar/keepalive-workflow@v1
-    - name: Setup Julia
-      uses: julia-actions/setup-julia@v1
+    - 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!!!!
+    - name: Download GenBank 
       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"), repos = "http://cran.us.r-project.org")'
-    - name: Download GenBank
-      run: |
-        Rscript -e 'source("Code/02_1a_Download GenBank.R")'
+        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")'
+        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
+    container: colebrookson/virion: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"), 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")'
@@ -85,15 +56,10 @@ jobs:
         path: Intermediate/Formatted/GLOBIFormatted.csv
   Finish:
     runs-on: ubuntu-latest
+    container: colebrookson/virion: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"), repos = "http://cran.us.r-project.org")'
     - name: Get GenBank
       uses: actions/download-artifact@v2
       with:

.gitignore

@@ -29,3 +29,4 @@ Intermediate/Formatted/GenbankFormatted.csv
 wc5/alt.bil
 wc5/alt.hdr
 Source/AllNuclMetadata.csv
+Source/AllNuclMetadata.csv.gz

Code/001_Julia functions.R

@@ -1,10 +1,14 @@
-library(tidyverse)
+#' Install Julia packages to use the functions for NCBI ========================
+#' 
+#' Here we use the JuliaCall library to get the funcitons we need 
+
+# create install.ncbi() function ===============================================
 
 install.ncbi <- function() {
-  library(JuliaCall)
-  julia_setup()
-  julia_install_package_if_needed("NCBITaxonomy")
-  julia_install_package_if_needed("DataFrames")
-  julia_install_package_if_needed("CSV")
-  julia_install_package_if_needed("ProgressMeter")
-}
+
+  # install the packages if needed 
+  JuliaCall::julia_install_package_if_needed("NCBITaxonomy") 
+  JuliaCall::julia_install_package_if_needed("DataFrames")
+  JuliaCall::julia_install_package_if_needed("CSV")
+  JuliaCall::julia_install_package_if_needed("ProgressMeter")
+}