From c81e466cb2284644d9d0bd7e1e668b30b79bc665 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 12 Jun 2017 14:18:43 -0500
Subject: Fix binary paths for GEMMA_COMMAND, PYLMM_COMMAND and PLINK_COMMAND

---
 wqflask/utility/tools.py | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 393ff2df..867bc5c8 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -108,13 +108,13 @@ def js_path(module=None):
     raise "No JS path found for "+module+" (check JS_GN_PATH)"
 
 def pylmm_command(guess=None):
-    return valid_bin(get_setting("PYLMM_COMMAND",guess))
+    return assert_bin(get_setting("PYLMM_COMMAND",guess))
 
 def gemma_command(guess=None):
-    return valid_bin(get_setting("GEMMA_COMMAND",guess))
+    return assert_bin(get_setting("GEMMA_COMMAND",guess))
 
 def plink_command(guess=None):
-    return valid_bin(get_setting("PLINK_COMMAND",guess))
+    return assert_bin(get_setting("PLINK_COMMAND",guess))
 
 def flat_file_exists(subdir):
     base = get_setting("GENENETWORK_FILES")
@@ -126,6 +126,11 @@ def flat_files(subdir=None):
         return assert_dir(base+"/"+subdir)
     return assert_dir(base)
 
+def assert_bin(fn):
+    if not valid_bin(fn):
+        raise Exception("ERROR: can not find binary "+fn)
+    return fn
+
 def assert_dir(dir):
     if not valid_path(dir):
         raise Exception("ERROR: can not find directory "+dir)
@@ -235,9 +240,9 @@ JS_GUIX_PATH       = get_setting('JS_GUIX_PATH')
 JS_GN_PATH         = get_setting('JS_GN_PATH')
 # assert_dir(JS_GN_PATH)
 
-PYLMM_COMMAND      = app_set("PYLMM_COMMAND",pylmm_command())
-GEMMA_COMMAND      = app_set("GEMMA_COMMAND",gemma_command())
-PLINK_COMMAND      = app_set("PLINK_COMMAND",plink_command())
+PYLMM_COMMAND      = pylmm_command()
+GEMMA_COMMAND      = gemma_command()
+PLINK_COMMAND      = plink_command()
 TEMPDIR            = tempdir() # defaults to UNIX TMPDIR
 
 # ---- Handle specific JS modules
-- 
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