[PATCH 041/100] Fixes for running tools

4 files changed, 10 insertions, 10 deletions

diff --git a/etc/default_settings.py b/etc/default_settings.py
index 6a218f26..60a3a7b4 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_COMMAND = os.popen("which pylmm_redis").read()
-PLINK_COMMAND = os.popen("which plink2").read()
-GEMMA_COMMAND = os.popen("which gemma").read()
+PYLMM_COMMAND = str.strip(os.popen("which pylmm_redis").read())
+PLINK_COMMAND = str.strip(os.popen("which plink2").read())
+GEMMA_COMMAND = str.strip(os.popen("which gemma").read())
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 67c5128a..51189fa3 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -133,7 +133,7 @@ def tempdir():
     
 # Cached values
 PYLMM_COMMAND = pylmm_command()
-GEMMA_COMMAND = pylmm_command()
-PLINK_COMMAND = pylmm_command()
+GEMMA_COMMAND = gemma_command()
+PLINK_COMMAND = plink_command()
 FLAT_FILES    = flat_files()
 TEMPDIR       = tempdir()
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 265f9473..910d0c3c 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -937,8 +937,7 @@ class MarkerRegression(object):
             Redis.expire(key, 60*60)
             print("before printing command")
 
-            command = PYLMM_COMMAND + ' --key {} --species {}'.format(key,
-                                                                                                                    "other")
+            command = PYLMM_COMMAND + ' --key {} --species {}'.format(key, "other")
             print("command is:", command)
             print("after printing command")
 
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index decde579..4edc1891 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -28,6 +28,7 @@ import time
 import string
 from math import *
 import piddle as pid
+import piddlePIL as pil
 import sys,os
 import cPickle
 import httplib, urllib
@@ -551,7 +552,7 @@ class MarkerRegression(object):
         #    showLocusForm =  webqtlUtil.genRandStr("fm_")
         #else:
         showLocusForm = ""
-        intCanvas = pid.PILCanvas(size=(self.graphWidth, self.graphHeight))
+        intCanvas = pil.PILCanvas(size=(self.graphWidth, self.graphHeight))
         gifmap = self.plotIntMapping(intCanvas, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm)
 
         self.gifmap = gifmap.__str__()
@@ -563,7 +564,7 @@ class MarkerRegression(object):
 
         #Scales plot differently for high resolution
         if self.draw2X:
-            intCanvasX2 = pid.PILCanvas(size=(self.graphWidth*2,self.graphHeight*2))
+            intCanvasX2 = pil.PILCanvas(size=(self.graphWidth*2,self.graphHeight*2))
             gifmapX2 = self.plotIntMapping(intCanvasX2, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm, zoom=2)
             intCanvasX2.save(os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, self.filename+"X2"), format='png')
             #DLintImgX2=HT.Href(text='Download',url = '/image/'+self.filename+'X2.png', Class='smallsize', target='_blank')
@@ -2582,7 +2583,7 @@ class MarkerRegression(object):
         #########################################
         #      Permutation Graph
         #########################################
-        myCanvas = pid.PILCanvas(size=(400,300))
+        myCanvas = pil.PILCanvas(size=(400,300))
         if 'lod_score' in self.qtlresults[0] and self.LRS_LOD == "LRS":
             perm_output = [value*4.16 for value in self.perm_output]
         elif 'lod_score' not in self.qtlresults[0] and self.LRS_LOD == "LOD":