From ee6dfff9769442c9ca15db43110c841fd5baac1f Mon Sep 17 00:00:00 2001
From: tjakobi <tjakobi@arizona.edu>
Date: Sat, 28 Sep 2024 20:32:14 +0200
Subject: [PATCH] Minimal R packages for circtest and primex

---
 circtools/scripts/install_R_dependencies.R | 55 +++++++++++++---------
 1 file changed, 32 insertions(+), 23 deletions(-)

diff --git a/circtools/scripts/install_R_dependencies.R b/circtools/scripts/install_R_dependencies.R
index f0405b4e1..e02bf0ae2 100755
--- a/circtools/scripts/install_R_dependencies.R
+++ b/circtools/scripts/install_R_dependencies.R
@@ -19,32 +19,41 @@ args <- commandArgs(trailingOnly = TRUE)
 base_path <- args[1]
 
 # we need these packages
+# pkgs <- c(
+#     "aod",
+#     "amap",
+#     "ballgown",
+#     "biomaRt",
+#     "data.table",
+#     "edgeR",
+#     "GenomicFeatures",
+#     "GenomicRanges",
+#     "ggbio",
+#     "ggfortify",
+#     "ggplot2",
+#     "gplots",
+#     "ggrepel",
+#     "gridExtra",
+#     "openxlsx",
+#     "plyr",
+#     "Hmisc",
+#     "reshape2",
+#     "devtools",
+#     "kableExtra",
+#     "formattable",
+#     "dplyr",
+#     "RColorBrewer"
+# )
+
 pkgs <- c(
-    "aod",
-    "amap",
-    "ballgown",
-    "biomaRt",
-    "data.table",
-    "edgeR",
-    "GenomicFeatures",
-    "GenomicRanges",
-    "ggbio",
-    "ggfortify",
-    "ggplot2",
-    "gplots",
-    "ggrepel",
-    "gridExtra",
-    "openxlsx",
-    "plyr",
-    "Hmisc",
-    "reshape2",
     "devtools",
-    "kableExtra",
-    "formattable",
-    "dplyr",
-    "RColorBrewer"
+    'GenomicRanges',
+    'ggplot2',
+    'BSgenome',
+    'IRanges',
+    'S4Vectors',
+    'Biostrings'
 )
-
 countdown <- function(from)
 {
   cat(from)