From 7cf6e44bcbea3cf451081bcc63375963e91708dc Mon Sep 17 00:00:00 2001 From: casanchez Date: Fri, 18 Oct 2024 10:40:28 -0400 Subject: [PATCH] installing rentrez package to fix pipeline --- .github/workflows/main.yml | 4 ++-- Code/02_1b_Digest GenBank.R | 1 + 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 8907c7e..ab73ee3 100644 --- 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 index c9808e3..be186d4 100644 --- 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")