3 files changed, 6 insertions, 6 deletions
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 6890dacf..0358bcbf 100755
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -56,9 +56,9 @@ UCSC_RUDI_TRACK_URL = " http://genome.cse.ucsc.edu/cgi-bin/hgTracks?org=%s&db=%s
 GENOMEBROWSER_URL="http://ucscbrowser.genenetwork.org/cgi-bin/hgTracks?clade=mammal&org=Mouse&db=mm9&position=%s&hgt.suggest=&pix=800&Submit=submit"
 ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Lucene/Details?species=Mus_musculus;idx=Transcript;end=1;q=%s"
 
-# HTMLPATH = GNROOT + 'genotype_files/'
-# PYLMM_PATH
-# IMGDIR = GNROOT + '/wqflask/wqflask/static/output/'
+# The following paths are no longer in use!
+#   HTMLPATH is replaced by GENODIR
+#   IMGDIR is replaced by GENERATED_IMAGE_DIR
 
 # Temporary storage:
 TMPDIR               = mk_dir(TEMPDIR+'/gn2/')
diff --git a/wqflask/wqflask/marker_regression/MarkerRegressionPage.py b/wqflask/wqflask/marker_regression/MarkerRegressionPage.py
index 455fcf95..4c3391e5 100755
--- a/wqflask/wqflask/marker_regression/MarkerRegressionPage.py
+++ b/wqflask/wqflask/marker_regression/MarkerRegressionPage.py
@@ -72,7 +72,7 @@ class MarkerRegressionPage(templatePage):
             #automatically generate pheno txt file for PLINK
             self.genPhenoTxtFileForPlink(phenoFileName=plinkOutputFileName,RISetName=fd.RISet,probesetName=probesetName, valueDict=allTraitValueDict)
             # os.system full path is required for input and output files; specify missing value is -9999
-            plink_command = '%splink/plink --noweb --ped %splink/%s.ped --no-fid --no-parents --no-sex --no-pheno --map %splink/%s.map --pheno %s/%s.txt --pheno-name %s --missing-phenotype -9999 --out %s%s --assoc ' % (webqtlConfig.HTMLPATH, webqtlConfig.HTMLPATH,  fd.RISet, webqtlConfig.HTMLPATH, fd.RISet, webqtlConfig.TMPDIR, plinkOutputFileName, probesetName, webqtlConfig.TMPDIR, plinkOutputFileName)
+            plink_command = '%splink/plink --noweb --ped %splink/%s.ped --no-fid --no-parents --no-sex --no-pheno --map %splink/%s.map --pheno %s/%s.txt --pheno-name %s --missing-phenotype -9999 --out %s%s --assoc ' % (webqtlConfig.GENODIR, webqtlConfig.GENODIR,  fd.RISet, webqtlConfig.GENODIR, fd.RISet, webqtlConfig.TMPDIR, plinkOutputFileName, probesetName, webqtlConfig.TMPDIR, plinkOutputFileName)
 
             os.system(plink_command)
 
@@ -1597,7 +1597,7 @@ class MarkerRegressionPage(templatePage):
 
     # get strain name from ped file in order
     def getStrainNameFromPedFile(self, RISetName=''):
-        pedFileopen= open("%splink/%s.ped"%(webqtlConfig.HTMLPATH, RISetName),"r")
+        pedFileopen= open("%splink/%s.ped"%(webqtlConfig.GENODIR, RISetName),"r")
         line =pedFileopen.readline()
         strainNameList=[]
 
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 8fb086c1..caea5802 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -11,7 +11,7 @@ def run_gemma(this_dataset, samples, vals):
     gen_pheno_txt_file(this_dataset, samples, vals)
 
     # Don't do this!
-    # os.chdir("{}gemma".format(webqtlConfig.HTMLPATH))
+    # os.chdir("{}gemma".format(webqtlConfig.GENODIR))
 
     # use GEMMA_RUN in the next one, create a unique temp file