scripts: Process R/qtl2 bundle

Build script to start the processing of the R/qtl2 bundle.

1 files changed, 4 insertions, 4 deletions

diff --git a/scripts/rqtl2/install_phenos.py b/scripts/rqtl2/install_phenos.py
index 5c25866..21b5f00 100644
--- a/scripts/rqtl2/install_phenos.py
+++ b/scripts/rqtl2/install_phenos.py
@@ -10,8 +10,8 @@ import MySQLdb as mdb
 from MySQLdb.cursors import DictCursor
 
 from scripts.rqtl2.entry import build_main
-from scripts.cli_parser import init_cli_parser
 from scripts.rqtl2.cli_parser import add_common_arguments
+from scripts.cli_parser import init_cli_parser, add_global_data_arguments
 
 from r_qtl import r_qtl2 as rqtl2
 
@@ -143,9 +143,9 @@ if __name__ == "__main__":
 
     def cli_args():
         """Process command-line arguments for `install_phenos`"""
-        parser = init_cli_parser(
+        parser = add_global_data_arguments(init_cli_parser(
             "install_genotypes",
-            "Parse genotypes from R/qtl2 bundle into the database.")
+            "Parse genotypes from R/qtl2 bundle into the database."))
 
         parser.add_argument(
             "platformid",
@@ -156,7 +156,7 @@ if __name__ == "__main__":
         return parser.parse_args()
 
     main = build_main(
-        cli_args,
+        cli_args(),
         lambda dbconn, args: install_pheno_files(dbconn,
                                                  args.speciesid,
                                                  args.platformid,