From 33bc6a57394f9fd3242a33e7cb29f01baa0692b1 Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Thu, 25 Feb 2016 13:32:58 +0000
Subject: More hard-coded

---
 wqflask/maintenance/gen_select_dataset.py              | 3 +--
 wqflask/wqflask/heatmap/heatmap.py                     | 5 +++--
 wqflask/wqflask/marker_regression/marker_regression.py | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index e080050e..489d291f 100755
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -36,8 +36,7 @@ from __future__ import print_function, division
 #print("cdict is:", cdict)
 
 import sys
-sys.path.append("/home/zas1024/")
-import zach_settings
+import zach_settings # no hard code paths!
 
 import MySQLdb
 
diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py
index 61847bc3..2445b37f 100644
--- a/wqflask/wqflask/heatmap/heatmap.py
+++ b/wqflask/wqflask/heatmap/heatmap.py
@@ -31,6 +31,7 @@ from base import species
 from utility import helper_functions
 from utility import Plot, Bunch
 from utility import temp_data
+from utility.tools import PYLMM_COMMAND
 
 from MySQLdb import escape_string as escape
 
@@ -212,7 +213,7 @@ class Heatmap(object):
             #Redis.expire(key, 60*60)
             #print("before printing command")
             #
-            #command = 'python /home/zas1024/gene/wqflask/wqflask/my_pylmm/pyLMM/lmm.py --key {} --species {}'.format(key,
+            #command = 'python lmm.py --key {} --species {}'.format(key,
             #                                                                                                        "other")
             #print("command is:", command)
             #print("after printing command")
@@ -271,7 +272,7 @@ class Heatmap(object):
             Redis.expire(key, 60*60)
             print("before printing command")
             
-            command = 'python /home/zas1024/gene/wqflask/wqflask/my_pylmm/pyLMM/lmm.py --key {} --species {}'.format(key,
+            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.py b/wqflask/wqflask/marker_regression/marker_regression.py
index d1c0d9bc..abd1ce85 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -318,7 +318,7 @@ class MarkerRegression(object):
                 outfile.write(str(sample) + " " + str(sample) + " 0 0 0 " + str(self.vals[i]) + "\n")
     
     def run_rqtl_plink(self):
-        # os.chdir("/home/zas1024/plink") never do this!!
+        # os.chdir("") never do this inside a webserver!!
         
         output_filename = webqtlUtil.genRandStr("%s_%s_"%(self.dataset.group.name, self.this_trait.name))
         
-- 
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