Added CLI R deps

bedboss/cli.py

@@ -556,6 +556,19 @@ def check_requirements():
     requirements_check()
 
 
+@app.command(help="Install R dependencies")
+def install_requirements():
+    import subprocess
+
+    r_path = os.path.abspath(
+        os.path.join(os.path.dirname(os.path.realpath(__file__)), "installRdeps.R")
+    )
+
+    subprocess.run(
+        ["Rscript", r_path],
+    )
+
+
 @app.callback()
 def common(
     ctx: typer.Context,

bedboss/installRdeps.R

@@ -0,0 +1,29 @@
+.install_pkg = function(p, bioc=FALSE) {
+    if(!require(package = p, character.only=TRUE)) {
+        if(bioc) {
+            BiocManager::install(pkgs = p)
+        } else {
+            install.packages(pkgs = p)   
+        }
+    }
+}
+
+.install_pkg("R.utils")
+.install_pkg("BiocManager")
+.install_pkg("optparse")
+.install_pkg("devtools")
+.install_pkg("GenomicRanges", bioc=TRUE)
+.install_pkg("GenomicFeatures", bioc=TRUE)
+.install_pkg("ensembldb", bioc=TRUE)
+.install_pkg("LOLA", bioc=TRUE)
+.install_pkg("BSgenome", bioc=TRUE)
+.install_pkg("ExperimentHub", bioc=TRUE)
+.install_pkg("AnnotationHub", bioc=TRUE)
+.install_pkg("conflicted")
+if(!require(package = "GenomicDistributions", character.only=TRUE)) {
+    devtools::install_github("databio/GenomicDistributions")
+}
+options(timeout=1000)
+if(!require(package = "GenomicDistributionsData", character.only=TRUE)) {
+    install.packages("http://big.databio.org/GenomicDistributionsData/GenomicDistributionsData_0.0.2.tar.gz", repos=NULL)
+}