Fetch RSCRIPT command from global environment variable.

* gn3/commands.py (compose_rqtl_cmd): Fetch RSCRIPT from global
environment.  Otherwise default to "Rscript".

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>

1 files changed, 3 insertions, 1 deletions

diff --git a/gn3/commands.py b/gn3/commands.py
index 9617663..74c634c 100644
--- a/gn3/commands.py
+++ b/gn3/commands.py
@@ -1,5 +1,6 @@
 """Procedures used to work with the various bio-informatics cli
 commands"""
+import os
 import sys
 import json
 import pickle
@@ -49,7 +50,8 @@ def compose_rqtl_cmd(rqtl_wrapper_cmd: str,
                      rqtl_wrapper_bool_kwargs: list) -> str:
     """Compose a valid R/qtl command given the correct input"""
     # Add kwargs with values
-    cmd = f"Rscript { rqtl_wrapper_cmd } " + " ".join(
+    rscript = os.environ.get("RSCRIPT", "Rscript")
+    cmd = f"{rscript} { rqtl_wrapper_cmd } " + " ".join(
         [f"--{key} {val}" for key, val in rqtl_wrapper_kwargs.items()])
 
     # Add boolean kwargs (kwargs that are either on or off, like --interval)