fixed r packages

ChiaraVanni · ChiaraVanni · commit b11bd3b8d537 · 2022-06-16T15:01:24.000+02:00
diff --git a/workflow/scripts/shadow_orfs.r b/workflow/scripts/shadow_orfs.r
@@ -10,6 +10,8 @@ if (!is.installed("valr")){
   cat("We will try to install the package... (this will be only be done once)\n")
   Sys.sleep(5)
   if (!is.installed("valr")){
+    suppressMessages(install.packages("BiocManager", repos = "http://cran.us.r-project.org"))
+    suppressMessages(BiocManager::install("rtracklayer"))
     suppressMessages(install.packages("valr", repos = "http://cran.us.r-project.org"))
   }
 }

Original file line number	Diff line number	Diff line change
`@@ -10,6 +10,8 @@ if (!is.installed("valr")){`
`10`	`10`	`cat("We will try to install the package... (this will be only be done once)\n")`
`11`	`11`	`Sys.sleep(5)`
`12`	`12`	`if (!is.installed("valr")){`
	`13`	`+ suppressMessages(install.packages("BiocManager", repos = "http://cran.us.r-project.org"))`
	`14`	`+ suppressMessages(BiocManager::install("rtracklayer"))`
`13`	`15`	`suppressMessages(install.packages("valr", repos = "http://cran.us.r-project.org"))`
`14`	`16`	`}`
`15`	`17`	`}`