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-rwxr-xr-xwqflask/maintenance/gen_select_dataset.py3
-rw-r--r--wqflask/wqflask/heatmap/heatmap.py5
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression.py2
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))