From 92fda7557645199276bf4f8a65c40252c4d83c21 Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Wed, 24 Feb 2016 09:25:43 +0000
Subject: Settled on the _COMMAND syntax over _RUN

---
 etc/default_settings.py  |  6 +++---
 wqflask/utility/tools.py | 10 +++-------
 2 files changed, 6 insertions(+), 10 deletions(-)

diff --git a/etc/default_settings.py b/etc/default_settings.py
index 48d3f66b..6a218f26 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -24,6 +24,6 @@ SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a
 
 # Path overrides for Genenetwork
 GENENETWORK_FILES = "../../gn2_data"
-PYLMM_RUN = os.popen("which pylmm_redis").read()
-PLINK_RUN = os.popen("which plink2").read()
-GEMMA_RUN = os.popen("which gemma").read()
+PYLMM_COMMAND = os.popen("which pylmm_redis").read()
+PLINK_COMMAND = os.popen("which plink2").read()
+GEMMA_COMMAND = os.popen("which gemma").read()
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index d4c10c68..0f2e4d88 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -1,9 +1,5 @@
 # Tools/paths finder resolves external paths from settings and/or environment
 # variables
-#
-# Currently supported:
-#
-#   PYLMM_PATH finds the root of the git repository of the pylmm_gn2 tool 
 
 import os
 import sys
@@ -69,13 +65,13 @@ def valid_path(dir):
     return None
 
 def pylmm_command(guess=None):
-    return valid_bin(get_setting("PYLMM_RUN",guess))
+    return valid_bin(get_setting("PYLMM_COMMAND",guess))
 
 def gemma_command(guess=None):
-    return valid_bin(get_setting("GEMMA_RUN",guess))
+    return valid_bin(get_setting("GEMMA_COMMAND",guess))
 
 def plink_command(guess=None):
-    return valid_bin(get_setting("PLINK_RUN",guess))
+    return valid_bin(get_setting("PLINK_COMMAND",guess))
 
 def flat_files(subdir=None):
     base = get_setting("GENENETWORK_FILES")
-- 
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