Add helper

Author: chartgerink

.DS_Store

@@ -1,4 +1,17 @@
-# Load configuration from config.yaml
+"""Testing GRAPEVNE
+
+This is a simple example module that demonstrates how to use GRAPEVNE modules. This module displays an image on the screen in a platform-independent way. The module touches an output file that we call a 'trigger' to signify that the module has completed successfully. The name of the trigger file is configurable.
+"""
+configfile: "config/config.yaml"
+from grapevne_helper import import_grapevne  # Import the bundled GRAPEVNE helper
+
+grapevne = import_grapevne(workflow)  # Use the helper to import GRAPEVNE
+                                      # You can specify version requirements here, e.g.
+                                      #  import_grapevne(workflow, version="0.2")
+
+globals().update(vars(grapevne))      # For convenience, we expose all variables from
+                                      # the GRAPEVNE module
+
 configfile: "config/config.yaml"
 
 # Rule to run the R script with the path parameter

workflows/.DS_Store

@@ -0,0 +1,25 @@
+import logging
+import sys
+
+try:
+    import grapevne
+except ImportError:
+    import ensurepip
+    import subprocess
+
+    ensurepip.bootstrap()
+    subprocess.check_call(
+        [sys.executable, "-m", "pip", "install", "--upgrade", "grapevne"]
+    )
+    try:
+        import grapevne
+    except ImportError:
+        logging.error("Failed to install grapevne. Exiting.")
+        sys.exit(1)
+
+
+def import_grapevne(workflow=None, version=None):
+    _grapevne = grapevne.install(version)
+    if workflow:
+        _grapevne.helpers.init(workflow)
+    return _grapevne.helpers