installing rentrez package to fix pipeline

viralemergence · Oct 18, 2024 · 7cf6e44 · 7cf6e44
1 parent 8c8e28e
commit 7cf6e44
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diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -33,7 +33,7 @@ jobs:
     - 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", "lubridate", "R.utils", "here", "JuliaCall"), repos = "http://cran.us.r-project.org")'
+        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")'
@@ -58,7 +58,7 @@ jobs:
     - 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", "lubridate", "tidyft", "here", "JuliaCall"), repos = "http://cran.us.r-project.org")'
+        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:

diff --git a/Code/02_1b_Digest GenBank.R b/Code/02_1b_Digest GenBank.R
@@ -6,6 +6,7 @@
 # set up =======================================================================
 
 library(magrittr)
+library(rentrez)
 
 # this is necessary for using the NCBI records of more than 10
 rentrez::set_entrez_key("ec345b39079e565bdfa744c3ef0d4b03ba08")