From 0f4ef95080697cb7fc1c4e30f4e5e3fb40ff5ab4 Mon Sep 17 00:00:00 2001
From: Thomas Weber <thomas.weber@embl.de>
Date: Fri, 22 Sep 2023 14:12:17 +0000
Subject: [PATCH] 2.2.2: install R package fix

---
 workflow/rules/setup.smk                   |  8 ++++----
 workflow/scripts/utils/install_R_package.R | 21 ++++++++++++++++-----
 2 files changed, 20 insertions(+), 9 deletions(-)

diff --git a/workflow/rules/setup.smk b/workflow/rules/setup.smk
index 5b381733..de8f3430 100644
--- a/workflow/rules/setup.smk
+++ b/workflow/rules/setup.smk
@@ -27,8 +27,8 @@ rule install_BSgenome_package:
         "../envs/rtools.yaml"
     resources:
         mem_mb=get_mem_mb_heavy,
-    script:
-        "../scripts/utils/install_R_package.R"
+    shell:
+        "Rscript workflow/scripts/utils/install_R_package.R {params.selected_package}"
 
 
 rule install_sctrip_multiplot_package:
@@ -44,8 +44,8 @@ rule install_sctrip_multiplot_package:
         "../envs/rtools.yaml"
     resources:
         mem_mb=get_mem_mb_heavy,
-    script:
-        "../scripts/utils/install_R_package.R"
+    shell:
+        "Rscript workflow/scripts/utils/install_R_package.R {params.selected_package}"
 
 
 rule config_run_summary:
diff --git a/workflow/scripts/utils/install_R_package.R b/workflow/scripts/utils/install_R_package.R
index eef070d3..ebf2e346 100644
--- a/workflow/scripts/utils/install_R_package.R
+++ b/workflow/scripts/utils/install_R_package.R
@@ -1,23 +1,34 @@
-package <- snakemake@params[["selected_package"]]
+# package <- snakemake@params[["selected_package"]]
+args <- commandArgs(TRUE)
+package <- args[1]
 
+# Check if the package is already available
 is_package_available <- require(package, character.only = TRUE)
 
 if (!isTRUE(is_package_available)) {
+    # Ensure BiocManager is available since it will be needed regardless of the condition
     if (!require("BiocManager", quietly = TRUE)) {
         install.packages("BiocManager", repos = "http://cran.us.r-project.org")
     }
 
+    # Condition 1: Install custom tar.gz Bsgenome package named BSgenome.T2T.CHM13.V2_1.0.0.tar.gz
     if (grepl("BSgenome.T2T.CHM13.V2_1.0.0.tar.gz", package, fixed = TRUE, perl = FALSE)) {
-        print("T2T")
         BiocManager::install("GenomeInfoDbData", update = FALSE)
         install.packages(package, repos = NULL, type = "source")
+
+        # Condition 2: Install standard Bsgenome packages (hg38/hg19/mm10)
+    } else if (package %in% c("BSgenome.Hsapiens.UCSC.hg38", "BSgenome.Hsapiens.UCSC.hg19", "BSgenome.Mmusculus.UCSC.mm10")) {
+        BiocManager::install(package, update = FALSE)
+
+        # Condition 3: Install a custom package using devtools
     } else {
-        # Check if devtools is installed, if not install it
+        # Ensure devtools is installed
         if (!require("devtools", quietly = TRUE)) {
             install.packages("devtools", repos = "http://cran.us.r-project.org")
         }
-        # Use devtools::install to install the package
         devtools::install(package, dependencies = TRUE, update = FALSE)
     }
-    quit(save = "no")
+
+    # Exit after installation, if desired
+    # quit(save = "no")
 }