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-rwxr-xr-xwqflask/base/data_set.py396
-rwxr-xr-xwqflask/base/webqtlConfig.py84
-rwxr-xr-xwqflask/base/webqtlFormData.py2
-rwxr-xr-xwqflask/basicStatistics/BasicStatisticsFunctions.py6
-rwxr-xr-xwqflask/maintenance/gen_select_dataset.py3
-rwxr-xr-xwqflask/maintenance/get_group_samplelists.py3
-rwxr-xr-xwqflask/runserver.py4
-rw-r--r--wqflask/utility/external.py9
-rw-r--r--wqflask/utility/genofile_parser.py100
-rw-r--r--wqflask/utility/tools.py189
-rwxr-xr-xwqflask/wqflask/correlation/show_corr_results.py14
-rwxr-xr-xwqflask/wqflask/correlation_matrix/show_corr_matrix.py1
-rwxr-xr-xwqflask/wqflask/ctl/__init__.py0
-rw-r--r--wqflask/wqflask/ctl/ctl_analysis.py194
-rwxr-xr-xwqflask/wqflask/database.py5
-rw-r--r--wqflask/wqflask/heatmap/heatmap.py7
-rwxr-xr-xwqflask/wqflask/interval_analyst/IntervalAnalystPage.py138
-rwxr-xr-xwqflask/wqflask/marker_regression/MarkerRegressionPage.py6
-rw-r--r--wqflask/wqflask/marker_regression/gemma_mapping.py11
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression.py87
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression_gn1.py129
-rwxr-xr-xwqflask/wqflask/search_results.py3
-rwxr-xr-xwqflask/wqflask/show_trait/show_trait.py13
l---------wqflask/wqflask/static/css1
-rw-r--r--wqflask/wqflask/static/dbdoc/TODO.md1
l---------wqflask/wqflask/static/images1
l---------wqflask/wqflask/static/javascript1
-rwxr-xr-xwqflask/wqflask/static/new/css/corr_matrix.css2
-rwxr-xr-xwqflask/wqflask/templates/collections/view.html12
-rw-r--r--wqflask/wqflask/templates/ctl_results.html47
-rw-r--r--wqflask/wqflask/templates/ctl_setup.html65
-rw-r--r--wqflask/wqflask/templates/marker_regression_gn1.html2
-rw-r--r--wqflask/wqflask/templates/wgcna_setup.html18
-rw-r--r--wqflask/wqflask/views.py27
-rw-r--r--wqflask/wqflask/wgcna/wgcna_analysis.py4
35 files changed, 935 insertions, 650 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index e37a838f..52ac95f0 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -44,6 +44,7 @@ from dbFunction import webqtlDatabaseFunction
 from utility import webqtlUtil
 from utility.benchmark import Bench
 from utility import chunks
+from utility.tools import locate, locate_ignore_error
 
 from maintenance import get_group_samplelists
 
@@ -57,40 +58,26 @@ DS_NAME_MAP = {}
 def create_dataset(dataset_name, dataset_type = None, get_samplelist = True):
     if not dataset_type:
         dataset_type = Dataset_Getter(dataset_name)
-        #dataset_type = get_dataset_type_from_json(dataset_name)
 
         print("dataset_type is:", dataset_type)
-        #query = """
-        #    SELECT DBType.Name
-        #    FROM DBList, DBType
-        #    WHERE DBList.Name = '{}' and
-        #          DBType.Id = DBList.DBTypeId
-        #    """.format(escape(dataset_name))
-        #dataset_type = g.db.execute(query).fetchone().Name
-
 
     dataset_ob = DS_NAME_MAP[dataset_type]
     dataset_class = globals()[dataset_ob]
     return dataset_class(dataset_name, get_samplelist)
 
-
-#def get_dataset_type_from_json(dataset_name):
-    
 class Dataset_Types(object):
-    
+
     def __init__(self):
         self.datasets = {}
         file_name = "wqflask/static/new/javascript/dataset_menu_structure.json"
         with open(file_name, 'r') as fh:
             data = json.load(fh)
-        
+
         print("*" * 70)
         for species in data['datasets']:
             for group in data['datasets'][species]:
                 for dataset_type in data['datasets'][species][group]:
                     for dataset in data['datasets'][species][group][dataset_type]:
-                        #print("dataset is:", dataset)
-                        
                         short_dataset_name = dataset[1]
                         if dataset_type == "Phenotypes":
                             new_type = "Publish"
@@ -99,32 +86,28 @@ class Dataset_Types(object):
                         else:
                             new_type = "ProbeSet"
                         self.datasets[short_dataset_name] = new_type
-                            
+
     def __call__(self, name):
         return self.datasets[name]
-    
+
 # Do the intensive work at startup one time only
 Dataset_Getter = Dataset_Types()
 
-#
-#print("Running at startup:", get_dataset_type_from_json("HBTRC-MLPFC_0611"))
-                    
-
 def create_datasets_list():
     key = "all_datasets"
     result = Redis.get(key)
-    
+
     if result:
         print("Cache hit!!!")
         datasets = pickle.loads(result)
-        
+
     else:
         datasets = list()
         with Bench("Creating DataSets object"):
             type_dict = {'Publish': 'PublishFreeze',
                          'ProbeSet': 'ProbeSetFreeze',
                          'Geno': 'GenoFreeze'}
-        
+
             for dataset_type in type_dict:
                 query = "SELECT Name FROM {}".format(type_dict[dataset_type])
                 for result in g.db.execute(query).fetchall():
@@ -133,10 +116,10 @@ def create_datasets_list():
                     #print("type: {}\tname: {}".format(dataset_type, result.Name))
                     dataset = create_dataset(result.Name, dataset_type)
                     datasets.append(dataset)
-            
+
         Redis.set(key, pickle.dumps(datasets, pickle.HIGHEST_PROTOCOL))
         Redis.expire(key, 60*60)
-    
+
     return datasets
 
 
@@ -157,30 +140,30 @@ def mescape(*items):
 class Markers(object):
     """Todo: Build in cacheing so it saves us reading the same file more than once"""
     def __init__(self, name):
-        json_data_fh = open(os.path.join(webqtlConfig.NEWGENODIR + name + '.json'))
+        json_data_fh = open(locate(name + '.json','genotype/json'))
         try:
             markers = json.load(json_data_fh)
         except:
             markers = []
-    
+
         for marker in markers:
             if (marker['chr'] != "X") and (marker['chr'] != "Y"):
                 marker['chr'] = int(marker['chr'])
             marker['Mb'] = float(marker['Mb'])
-            
+
         self.markers = markers
         #print("self.markers:", self.markers)
-    
-    
+
+
     def add_pvalues(self, p_values):
         print("length of self.markers:", len(self.markers))
         print("length of p_values:", len(p_values))
-        
+
         if type(p_values) is list:
             # THIS IS only needed for the case when we are limiting the number of p-values calculated
             #if len(self.markers) > len(p_values):
             #    self.markers = self.markers[:len(p_values)]
-            
+
             for marker, p_value in itertools.izip(self.markers, p_values):
                 if not p_value:
                     continue
@@ -213,18 +196,11 @@ class Markers(object):
                     #self.markers.remove(marker)
                     #del self.markers[i]
             self.markers = filtered_markers
-            
-
-        #for i, marker in enumerate(self.markers):
-        #    if not 'p_value' in marker:
-        #        #print("self.markers[i]", self.markers[i])
-        #        del self.markers[i]
-        #        #self.markers.remove(self.markers[i])
 
 class HumanMarkers(Markers):
-    
+
     def __init__(self, name, specified_markers = []):
-        marker_data_fh = open(os.path.join(webqtlConfig.PYLMM_PATH + name + '.bim'))
+        marker_data_fh = open(locate('genotype') + '/' + name + '.bim')
         self.markers = []
         for line in marker_data_fh:
             splat = line.strip().split()
@@ -243,39 +219,21 @@ class HumanMarkers(Markers):
                 marker['name'] = splat[1]
                 marker['Mb'] = float(splat[3]) / 1000000
             self.markers.append(marker)
-            
+
         #print("markers is: ", pf(self.markers))
 
 
     def add_pvalues(self, p_values):
-        #for marker, p_value in itertools.izip(self.markers, p_values):
-        #    if marker['Mb'] <= 0 and marker['chr'] == 0:
-        #        continue
-        #    marker['p_value'] = p_value
-        #    print("p_value is:", marker['p_value'])
-        #    marker['lod_score'] = -math.log10(marker['p_value'])
-        #    #Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values
-        #    marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61
-        
-        #print("p_values2:", pf(p_values))
         super(HumanMarkers, self).add_pvalues(p_values)
-        
-        #with Bench("deleting markers"):
-        #    markers = []
-        #    for marker in self.markers:
-        #        if not marker['Mb'] <= 0 and not marker['chr'] == 0:
-        #            markers.append(marker)
-        #    self.markers = markers
-        
-    
+
 
 class DatasetGroup(object):
     """
     Each group has multiple datasets; each species has multiple groups.
-    
+
     For example, Mouse has multiple groups (BXD, BXA, etc), and each group
     has multiple datasets associated with it.
-    
+
     """
     def __init__(self, dataset):
         """This sets self.group and self.group_id"""
@@ -283,14 +241,14 @@ class DatasetGroup(object):
         self.name, self.id = g.db.execute(dataset.query_for_group).fetchone()
         if self.name == 'BXD300':
             self.name = "BXD"
-        
+
         self.f1list = None
         self.parlist = None
         self.get_f1_parent_strains()
         #print("parents/f1s: {}:{}".format(self.parlist, self.f1list))
-        
+
         self.species = webqtlDatabaseFunction.retrieve_species(self.name)
-        
+
         self.incparentsf1 = False
         self.allsamples = None
         self._datasets = None
@@ -301,7 +259,7 @@ class DatasetGroup(object):
     def get_markers(self):
         #print("self.species is:", self.species)
         if self.species == "human":
-            marker_class = HumanMarkers 
+            marker_class = HumanMarkers
         else:
             marker_class = Markers
 
@@ -310,12 +268,6 @@ class DatasetGroup(object):
     def datasets(self):
         key = "group_dataset_menu:v2:" + self.name
         print("key is2:", key)
-        #with Bench("Loading cache"):
-        #    result = Redis.get(key)
-        #if result:
-        #    self._datasets = pickle.loads(result)
-        #    return self._datasets
-
         dataset_menu = []
         print("[tape4] webqtlConfig.PUBLICTHRESH:", webqtlConfig.PUBLICTHRESH)
         print("[tape4] type webqtlConfig.PUBLICTHRESH:", type(webqtlConfig.PUBLICTHRESH))
@@ -355,7 +307,7 @@ class DatasetGroup(object):
                 dataset_menu.append(dict(tissue=None, datasets=[(dataset, dataset_short)]))
             else:
                 dataset_sub_menu = [item[1:] for item in dataset]
-                
+
                 tissue_already_exists = False
                 tissue_position = None
                 for i, tissue_dict in enumerate(dataset_menu):
@@ -383,7 +335,7 @@ class DatasetGroup(object):
             f1, f12, maternal, paternal = webqtlUtil.ParInfo[self.name]
         except KeyError:
             f1 = f12 = maternal = paternal = None
-            
+
         if f1 and f12:
             self.f1list = [f1, f12]
         if maternal and paternal:
@@ -402,21 +354,17 @@ class DatasetGroup(object):
             #print("  type: ", type(self.samplelist))
             #print("  self.samplelist: ", self.samplelist)
         else:
-            #print("Cache not hit")
-
-            from utility.tools import plink_command
-            PLINK_PATH,PLINK_COMMAND = plink_command()
-
-            geno_file_path = webqtlConfig.GENODIR+self.name+".geno"
-            plink_file_path = PLINK_PATH+"/"+self.name+".fam"
-
-            if os.path.isfile(plink_file_path):
-                self.samplelist = get_group_samplelists.get_samplelist("plink", plink_file_path)
-            elif os.path.isfile(geno_file_path):
-                self.samplelist = get_group_samplelists.get_samplelist("geno", geno_file_path)
+            print("Cache not hit")
+
+            genotype_fn = locate_ignore_error(self.name+".geno",'genotype')
+            mapping_fn = locate_ignore_error(self.name+".fam",'mapping')
+            if mapping_fn:
+                self.samplelist = get_group_samplelists.get_samplelist("plink", mapping_fn)
+            elif genotype_fn:
+                self.samplelist = get_group_samplelists.get_samplelist("geno", genotype_fn)
             else:
                 self.samplelist = None
-            #print("after get_samplelist")
+            print("Sample list: ",self.samplelist)
             Redis.set(key, json.dumps(self.samplelist))
             Redis.expire(key, 60*5)
 
@@ -428,30 +376,14 @@ class DatasetGroup(object):
 
     def read_genotype_file(self):
         '''Read genotype from .geno file instead of database'''
-        #if self.group == 'BXD300':
-        #    self.group = 'BXD'
-        #
-        #assert self.group, "self.group needs to be set"
-
         #genotype_1 is Dataset Object without parents and f1
         #genotype_2 is Dataset Object with parents and f1 (not for intercross)
 
         genotype_1 = reaper.Dataset()
 
         # reaper barfs on unicode filenames, so here we ensure it's a string
-        full_filename = str(os.path.join(webqtlConfig.GENODIR, self.name + '.geno'))
-        if os.path.isfile(full_filename):
-            #print("Reading file: ", full_filename)
-            genotype_1.read(full_filename)
-            #print("File read")
-        else:
-            try:
-                full_filename = str(os.path.join(webqtlConfig.TMPDIR, self.name + '.geno'))
-                #print("Reading file")
-                genotype_1.read(full_filename)
-                #print("File read")
-            except IOError:
-                print("File doesn't exist!")
+        full_filename = str(locate(self.name+'.geno','genotype'))
+        genotype_1.read(full_filename)
 
         if genotype_1.type == "group" and self.parlist:
             genotype_2 = genotype_1.add(Mat=self.parlist[0], Pat=self.parlist[1])       #, F1=_f1)
@@ -460,39 +392,15 @@ class DatasetGroup(object):
 
         #determine default genotype object
         if self.incparentsf1 and genotype_1.type != "intercross":
-            #self.genotype = genotype_2
             genotype = genotype_2
         else:
             self.incparentsf1 = 0
-            #self.genotype = genotype_1
             genotype = genotype_1
 
-        #self.samplelist = list(self.genotype.prgy)
         self.samplelist = list(genotype.prgy)
-        
-        return genotype
-
-
-#class DataSets(object):
-#    """Builds a list of DataSets"""
-#    
-#    def __init__(self):
-#        self.datasets = list()
-#        
 
-        
-        #query = """SELECT Name FROM ProbeSetFreeze
-        #           UNION
-        #           SELECT Name From PublishFreeze
-        #           UNION
-        #           SELECT Name From GenoFreeze"""
-        #
-        #for result in g.db.execute(query).fetchall():
-        #    dataset = DataSet(result.Name)
-        #    self.datasets.append(dataset)
+        return genotype
 
-#ds = DataSets()
-#print("[orange] ds:", ds.datasets)
 
 class DataSet(object):
     """
@@ -515,7 +423,7 @@ class DataSet(object):
         self.check_confidentiality()
 
         self.retrieve_other_names()
-        
+
         self.group = DatasetGroup(self)   # sets self.group and self.group_id and gets genotype
         if get_samplelist == True:
              self.group.get_samplelist()
@@ -525,32 +433,11 @@ class DataSet(object):
     def get_desc(self):
         """Gets overridden later, at least for Temp...used by trait's get_given_name"""
         return None
-    
-    #@staticmethod
-    #def get_by_trait_id(trait_id):
-    #    """Gets the dataset object given the trait id"""
-    #    
-    #    
-    #
-    #    name = g.db.execute(""" SELECT 
-    #                        
-    #                        """)
-    #    
-    #    return DataSet(name)
 
     # Delete this eventually
     @property
     def riset():
         Weve_Renamed_This_As_Group
-        
-        
-    #@property
-    #def group(self):
-    #    if not self._group:
-    #        self.get_group()
-    #        
-    #    return self._group
-
 
     def retrieve_other_names(self):
         """
@@ -560,7 +447,7 @@ class DataSet(object):
         This is not meant to retrieve the data set info if no name at all is passed.
 
         """
-        
+
         try:
             if self.type == "ProbeSet":
                 query_args = tuple(escape(x) for x in (
@@ -596,17 +483,17 @@ class DataSet(object):
         except TypeError:
             print("Dataset {} is not yet available in GeneNetwork.".format(self.name))
             pass
-        
+
     def get_trait_data(self, sample_list=None):
         if sample_list:
             self.samplelist = sample_list
         else:
             self.samplelist = self.group.samplelist
-            
+
         if self.group.parlist != None and self.group.f1list != None:
             if (self.group.parlist + self.group.f1list) in self.samplelist:
                 self.samplelist += self.group.parlist + self.group.f1list
-        
+
         query = """
             SELECT Strain.Name, Strain.Id FROM Strain, Species
             WHERE Strain.Name IN {}
@@ -623,21 +510,6 @@ class DataSet(object):
         number_chunks = int(math.ceil(len(sample_ids) / chunk_size))
         trait_sample_data = []
         for sample_ids_step in chunks.divide_into_chunks(sample_ids, number_chunks):
-
-        #XZ, 09/24/2008: build one temporary table that only contains the records associated with the input GeneId 
-        #tempTable = None
-        #if GeneId and db.type == "ProbeSet": 
-        #    if method == "3":
-        #        tempTable = self.getTempLiteratureTable(species=species,
-        #                                                input_species_geneid=GeneId,
-        #                                                returnNumber=returnNumber)
-        #
-        #    if method == "4" or method == "5":
-        #        tempTable = self.getTempTissueCorrTable(primaryTraitSymbol=GeneSymbol,
-        #                                        TissueProbeSetFreezeId=tissueProbeSetFreezeId,
-        #                                        method=method,
-        #                                        returnNumber=returnNumber)
-        
             if self.type == "Publish":
                 dataset_type = "Phenotype"
             else:
@@ -658,7 +530,7 @@ class DataSet(object):
                         left join {}Data as T{} on T{}.Id = {}XRef.DataId
                         and T{}.StrainId={}\n
                         """.format(*mescape(self.type, item, item, self.type, item, item))
-                        
+
             if self.type == "Publish":
                 query += """
                         WHERE {}XRef.InbredSetId = {}Freeze.InbredSetId
@@ -675,16 +547,16 @@ class DataSet(object):
                         order by {}.Id
                         """.format(*mescape(self.type, self.type, self.type, self.type,
                                    self.name, dataset_type, self.type, self.type, dataset_type))
-                        
+
             #print("trait data query: ", query)
-            
+
             results = g.db.execute(query).fetchall()
             #print("query results:", results)
             trait_sample_data.append(results)
 
         trait_count = len(trait_sample_data[0])
         self.trait_data = collections.defaultdict(list)
-        
+
         # put all of the separate data together into a dictionary where the keys are
         # trait names and values are lists of sample values
         for trait_counter in range(trait_count):
@@ -697,9 +569,9 @@ class PhenotypeDataSet(DataSet):
     DS_NAME_MAP['Publish'] = 'PhenotypeDataSet'
 
     def setup(self):
-        
+
         #print("IS A PHENOTYPEDATASET")
-        
+
         # Fields in the database table
         self.search_fields = ['Phenotype.Post_publication_description',
                             'Phenotype.Pre_publication_description',
@@ -770,26 +642,26 @@ class PhenotypeDataSet(DataSet):
 
     def get_trait_info(self, trait_list, species = ''):
         for this_trait in trait_list:
-            
+
             if not this_trait.haveinfo:
                 this_trait.retrieve_info(get_qtl_info=True)
 
             description = this_trait.post_publication_description
-            
+
             #If the dataset is confidential and the user has access to confidential
             #phenotype traits, then display the pre-publication description instead
             #of the post-publication description
             if this_trait.confidential:
                 this_trait.description_display = ""
                 continue   # for now
-            
+
                 if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(
                         privilege=self.privilege,
                         userName=self.userName,
                         authorized_users=this_trait.authorized_users):
-                        
+
                     description = this_trait.pre_publication_description
-            
+
             if len(description) > 0:
                 this_trait.description_display = description.strip()
             else:
@@ -834,7 +706,7 @@ class PhenotypeDataSet(DataSet):
                         this_trait.LRS_score_repr = LRS_score_repr = '%3.1f' % this_trait.lrs
                         this_trait.LRS_score_value = LRS_score_value = this_trait.lrs
                         this_trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (LRS_Chr, float(LRS_Mb))
-                        
+
     def retrieve_sample_data(self, trait):
         query = """
                     SELECT
@@ -892,7 +764,7 @@ class GenotypeDataSet(DataSet):
 
     def check_confidentiality(self):
         return geno_mrna_confidentiality(self)
-    
+
     def get_trait_list(self):
         query = """
             select Geno.Name
@@ -926,7 +798,7 @@ class GenotypeDataSet(DataSet):
 
                 this_trait.location_repr = 'Chr%s: %.6f' % (this_trait.chr, float(this_trait.mb) )
                 this_trait.location_value = trait_location_value
-                
+
     def retrieve_sample_data(self, trait):
         query = """
                     SELECT
@@ -1018,7 +890,7 @@ class MrnaAssayDataSet(DataSet):
 
     def check_confidentiality(self):
         return geno_mrna_confidentiality(self)
-        
+
     def get_trait_list_1(self):
         query = """
             select ProbeSet.Name
@@ -1027,86 +899,14 @@ class MrnaAssayDataSet(DataSet):
             and ProbeSetFreezeId = {}
             """.format(escape(str(self.id)))
         results = g.db.execute(query).fetchall()
-        #print("After get_trait_list query")
         trait_data = {}
         for trait in results:
-            #print("Retrieving sample_data for ", trait[0])
             trait_data[trait[0]] = self.retrieve_sample_data(trait[0])
-        #print("After retrieve_sample_data")
         return trait_data
-    
-    #def get_trait_data(self):
-    #    self.samplelist = self.group.samplelist + self.group.parlist + self.group.f1list
-    #    query = """
-    #        SELECT Strain.Name, Strain.Id FROM Strain, Species
-    #        WHERE Strain.Name IN {}
-    #        and Strain.SpeciesId=Species.Id
-    #        and Species.name = '{}'
-    #        """.format(create_in_clause(self.samplelist), *mescape(self.group.species))
-    #    results = dict(g.db.execute(query).fetchall())
-    #    sample_ids = [results[item] for item in self.samplelist]
-    #
-    #    # MySQL limits the number of tables that can be used in a join to 61,
-    #    # so we break the sample ids into smaller chunks
-    #    # Postgres doesn't have that limit, so we can get rid of this after we transition
-    #    chunk_size = 50
-    #    number_chunks = int(math.ceil(len(sample_ids) / chunk_size))
-    #    trait_sample_data = []
-    #    for sample_ids_step in chunks.divide_into_chunks(sample_ids, number_chunks):
-    #
-    #    #XZ, 09/24/2008: build one temporary table that only contains the records associated with the input GeneId 
-    #    #tempTable = None
-    #    #if GeneId and db.type == "ProbeSet": 
-    #    #    if method == "3":
-    #    #        tempTable = self.getTempLiteratureTable(species=species,
-    #    #                                                input_species_geneid=GeneId,
-    #    #                                                returnNumber=returnNumber)
-    #    #
-    #    #    if method == "4" or method == "5":
-    #    #        tempTable = self.getTempTissueCorrTable(primaryTraitSymbol=GeneSymbol,
-    #    #                                        TissueProbeSetFreezeId=tissueProbeSetFreezeId,
-    #    #                                        method=method,
-    #    #                                        returnNumber=returnNumber)
-    #    
-    #        temp = ['T%s.value' % item for item in sample_ids_step]
-    #        query = "SELECT {}.Name,".format(escape(self.type))
-    #        data_start_pos = 1
-    #        query += string.join(temp, ', ')
-    #        query += ' FROM ({}, {}XRef, {}Freeze) '.format(*mescape(self.type,
-    #                                                                 self.type,
-    #                                                                 self.type))
-    #
-    #        for item in sample_ids_step:
-    #            query += """
-    #                    left join {}Data as T{} on T{}.Id = {}XRef.DataId
-    #                    and T{}.StrainId={}\n
-    #                    """.format(*mescape(self.type, item, item, self.type, item, item))
-    #                    
-    #        query += """
-    #                WHERE {}XRef.{}FreezeId = {}Freeze.Id
-    #                and {}Freeze.Name = '{}'
-    #                and {}.Id = {}XRef.{}Id
-    #                order by {}.Id
-    #                """.format(*mescape(self.type, self.type, self.type, self.type,
-    #                           self.name, self.type, self.type, self.type, self.type))
-    #        results = g.db.execute(query).fetchall()
-    #        trait_sample_data.append(results)
-    #
-    #    trait_count = len(trait_sample_data[0])
-    #    self.trait_data = collections.defaultdict(list)
-    #    
-    #    # put all of the separate data together into a dictionary where the keys are
-    #    # trait names and values are lists of sample values
-    #    for trait_counter in range(trait_count):
-    #        trait_name = trait_sample_data[0][trait_counter][0]
-    #        for chunk_counter in range(int(number_chunks)):
-    #            self.trait_data[trait_name] += (
-    #                trait_sample_data[chunk_counter][trait_counter][data_start_pos:])
-    
 
     def get_trait_info(self, trait_list=None, species=''):
 
-        #  Note: setting trait_list to [] is probably not a great idea. 
+        #  Note: setting trait_list to [] is probably not a great idea.
         if not trait_list:
             trait_list = []
 
@@ -1169,7 +969,7 @@ class MrnaAssayDataSet(DataSet):
             #print("query is:", pf(query))
 
             result = g.db.execute(query).fetchone()
-            
+
             mean = result[0] if result else 0
 
             if mean:
@@ -1190,28 +990,15 @@ class MrnaAssayDataSet(DataSet):
                         Geno.SpeciesId = Species.Id
                 """.format(species, this_trait.locus)
                 result = g.db.execute(query).fetchone()
-                
+
                 if result:
-                    #if result[0] and result[1]:
-                    #    lrs_chr = result[0]
-                    #    lrs_mb = result[1]
                     lrs_chr, lrs_mb = result
                     #XZ: LRS_location_value is used for sorting
                     lrs_location_value = self.convert_location_to_value(lrs_chr, lrs_mb)
-                    
-                    #try:
-                    #    lrs_location_value = int(lrs_chr)*1000 + float(lrs_mb)
-                    #except:
-                    #    if lrs_chr.upper() == 'X':
-                    #        lrs_location_value = 20*1000 + float(lrs_mb)
-                    #    else:
-                    #        lrs_location_value = (ord(str(LRS_chr).upper()[0])*1000 +
-                    #                              float(lrs_mb))
-
                     this_trait.LRS_score_repr = '%3.1f' % this_trait.lrs
                     this_trait.LRS_score_value = this_trait.lrs
                     this_trait.LRS_location_repr = 'Chr%s: %.6f' % (lrs_chr, float(lrs_mb))
-      
+
 
     def convert_location_to_value(self, chromosome, mb):
         try:
@@ -1222,7 +1009,7 @@ class MrnaAssayDataSet(DataSet):
             else:
                 location_value = (ord(str(chromosome).upper()[0])*1000 +
                                   float(mb))
-        
+
         return location_value
 
     def get_sequence(self):
@@ -1239,7 +1026,7 @@ class MrnaAssayDataSet(DataSet):
                 """ % (escape(self.name), escape(self.dataset.name))
         results = g.db.execute(query).fetchone()
         return results[0]
-   
+
     def retrieve_sample_data(self, trait):
         query = """
                     SELECT
@@ -1260,8 +1047,8 @@ class MrnaAssayDataSet(DataSet):
         results = g.db.execute(query).fetchall()
         #print("RETRIEVED RESULTS HERE:", results)
         return results
-    
-    
+
+
     def retrieve_genes(self, column_name):
         query = """
                     select ProbeSet.Name, ProbeSet.%s
@@ -1270,37 +1057,8 @@ class MrnaAssayDataSet(DataSet):
                     ProbeSetXRef.ProbeSetId=ProbeSet.Id;
                 """ % (column_name, escape(str(self.id)))
         results = g.db.execute(query).fetchall()
-        
-        return dict(results)
 
-    #def retrieve_gene_symbols(self):
-    #    query = """
-    #                select ProbeSet.Name, ProbeSet.Symbol, ProbeSet.GeneId
-    #                from ProbeSet,ProbeSetXRef
-    #                where ProbeSetXRef.ProbeSetFreezeId = %s and
-    #                ProbeSetXRef.ProbeSetId=ProbeSet.Id;
-    #            """ % (self.id)
-    #    results = g.db.execute(query).fetchall()
-    #    symbol_dict = {}
-    #    for item in results:
-    #        symbol_dict[item[0]] = item[1]
-    #    return symbol_dict
-    #
-    #def retrieve_gene_ids(self):
-    #    query = """
-    #                select ProbeSet.Name, ProbeSet.GeneId
-    #                from ProbeSet,ProbeSetXRef
-    #                where ProbeSetXRef.ProbeSetFreezeId = %s and
-    #                ProbeSetXRef.ProbeSetId=ProbeSet.Id;
-    #            """ % (self.id)
-    #    return process_and_run_query(query)
-    #    results = g.db.execute(query).fetchall()
-    #    symbol_dict = {}
-    #    for item in results:
-    #        symbol_dict[item[0]] = item[1]
-    #    return symbol_dict
-    
-    
+        return dict(results)
 
 
 class TempDataSet(DataSet):
@@ -1322,8 +1080,8 @@ class TempDataSet(DataSet):
         self.id = 1
         self.fullname = 'Temporary Storage'
         self.shortname = 'Temp'
-        
-       
+
+
     @staticmethod
     def handle_pca(desc):
         if 'PCA' in desc:
@@ -1332,13 +1090,13 @@ class TempDataSet(DataSet):
         else:
             desc = desc[:desc.index('entered')].strip()
         return desc
-        
+
     def get_desc(self):
         g.db.execute('SELECT description FROM Temp WHERE Name=%s', self.name)
         desc = g.db.fetchone()[0]
         desc = self.handle_pca(desc)
-        return desc    
-        
+        return desc
+
     def get_group(self):
         self.cursor.execute("""
                     SELECT
@@ -1351,7 +1109,7 @@ class TempDataSet(DataSet):
             """, self.name)
         self.group, self.group_id = self.cursor.fetchone()
         #return self.group
-        
+
     def retrieve_sample_data(self, trait):
         query = """
                 SELECT
@@ -1365,7 +1123,7 @@ class TempDataSet(DataSet):
                 Order BY
                         Strain.Name
                 """ % escape(trait.name)
-                
+
         results = g.db.execute(query).fetchall()
 
 
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
new file mode 100755
index 00000000..cdce119a
--- /dev/null
+++ b/wqflask/base/webqtlConfig.py
@@ -0,0 +1,84 @@
+#########################################'
+#      Environment Variables - public
+#
+# Note: much of this needs to handled by the settings/environment
+# scripts. But rather than migrating everything in one go, we'll
+# take it a step at a time. First the hard coded paths get replaced
+# with those in utility/tools.py
+# 
+#########################################
+
+from utility.tools import mk_dir, assert_dir, flat_files, TEMPDIR
+
+#Debug Level
+#1 for debug, mod python will reload import each time
+DEBUG = 1
+
+#USER privilege
+USERDICT = {'guest':1,'user':2, 'admin':3, 'root':4}
+
+#minimum number of informative strains
+KMININFORMATIVE = 5
+
+#maximum number of traits for interval mapping
+MULTIPLEMAPPINGLIMIT = 11
+
+#maximum number of traits for correlation
+MAXCORR = 100
+
+#Daily download limit from one IP
+DAILYMAXIMUM = 1000
+
+#maximum LRS value
+MAXLRS = 460.0
+
+#temporary data life span
+MAXLIFE = 86400
+
+#MINIMUM Database public value
+PUBLICTHRESH = 0
+
+#NBCI address
+NCBI_LOCUSID = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s"
+UCSC_REFSEQ = "http://genome.cse.ucsc.edu/cgi-bin/hgGene?db=%s&hgg_gene=%s&hgg_chrom=chr%s&hgg_start=%s&hgg_end=%s"
+GENBANK_ID = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=search&doptcmdl=DocSum&term=%s"
+OMIM_ID = "http://www.ncbi.nlm.nih.gov/omim/%s"
+UNIGEN_ID = "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=%s&CID=%s";
+HOMOLOGENE_ID = "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=homologene&Cmd=DetailsSearch&Term=%s"
+PUBMEDLINK_URL = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=%s&dopt=Abstract"
+UCSC_POS = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=mammal&org=%s&db=%s&position=chr%s:%s-%s&pix=800&Submit=submit"
+UCSC_BLAT = 'http://genome.ucsc.edu/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s'
+UTHSC_BLAT = 'http://ucscbrowser.genenetwork.org/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s'
+UCSC_GENOME = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d&hgt.customText=http://web2qtl.utmem.edu:88/snp/chr%s"
+ENSEMBLE_BLAT = 'http://www.ensembl.org/Mus_musculus/featureview?type=AffyProbe&id=%s'
+DBSNP = 'http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=%s'
+UCSC_RUDI_TRACK_URL = " http://genome.cse.ucsc.edu/cgi-bin/hgTracks?org=%s&db=%s&hgt.customText=http://gbic.biol.rug.nl/~ralberts/tracks/%s/%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/'
+
+# Temporary storage:
+TMPDIR               = mk_dir(TEMPDIR+'/gn2/')
+CACHEDIR             = mk_dir(TEMPDIR+'/cache/')
+# We can no longer write into the git tree:
+GENERATED_IMAGE_DIR  = mk_dir(TMPDIR+'/generate/')
+GENERATED_TEXT_DIR   = mk_dir(TMPDIR+'/generate_text/')
+
+# Flat file directories
+GENODIR              = flat_files('genotype')+'/'
+JSON_GENODIR         = assert_dir(GENODIR+'json/')
+
+# SITENAME = 'GN'
+# PORTADDR = "http://50.16.251.170"
+# BASEHREF = '<base href="http://50.16.251.170/">'
+
+INFOPAGEHREF = '/dbdoc/%s.html'
+CGIDIR = '/webqtl/' #XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR'
+SCRIPTFILE = 'main.py'
+
+# GLOSSARYFILE = "/glossary.html"
+# REFRESHSTR = '<meta http-equiv="refresh" content="5;url=%s' + SCRIPTFILE +'?sid=%s">'
+# REFRESHDIR = '%s' + SCRIPTFILE +'?sid=%s'
diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py
index 44fdcc3f..10251756 100755
--- a/wqflask/base/webqtlFormData.py
+++ b/wqflask/base/webqtlFormData.py
@@ -157,7 +157,7 @@ class webqtlFormData(object):
 
         self.genotype_1 = reaper.Dataset()
 
-        full_filename = os.path.join(webqtlConfig.GENODIR, self.group + '.geno')
+        full_filename = locate(self.group + '.geno','genotype')
 
         # reaper barfs on unicode filenames, so here we ensure it's a string
         full_filename = str(full_filename)
diff --git a/wqflask/basicStatistics/BasicStatisticsFunctions.py b/wqflask/basicStatistics/BasicStatisticsFunctions.py
index 74784853..e748a822 100755
--- a/wqflask/basicStatistics/BasicStatisticsFunctions.py
+++ b/wqflask/basicStatistics/BasicStatisticsFunctions.py
@@ -118,7 +118,7 @@ def plotNormalProbability(vals=None, RISet='', title=None, showstrains=0, specia
     Plot.plotXY(c, dataZ, dataX, dataLabel = dataLabel, XLabel='Expected Z score', connectdot=0, YLabel='Trait value', title=title, specialCases=specialStrains, showLabel = showLabel)
 
     filename= webqtlUtil.genRandStr("nP_")
-    c.save(webqtlConfig.IMGDIR+filename, format='gif')
+    c.save(webqtlConfig.GENERATED_IMAGE_DIR+filename, format='gif')
 
     img=HT.Image('/image/'+filename+'.gif',border=0)
 
@@ -145,7 +145,7 @@ def plotBoxPlot(vals):
 
     Plot.plotBoxPlot(canvas, XXX, offset=(xLeftOffset, xRightOffset, yTopOffset, yBottomOffset), XLabel= "Trait")
     filename= webqtlUtil.genRandStr("Box_")
-    canvas.save(webqtlConfig.IMGDIR+filename, format='gif')
+    canvas.save(webqtlConfig.GENERATED_IMAGE_DIR+filename, format='gif')
     img=HT.Image('/image/'+filename+'.gif',border=0)
 
     plotLink = HT.Span("More about ", HT.Href(text="Box Plots", url="http://davidmlane.com/hyperstat/A37797.html", target="_blank", Class="fs13"))
@@ -201,7 +201,7 @@ def plotBarGraph(identification='', RISet='', vals=None, type="name"):
     Plot.plotBarText(c, tvals, tnames, variance=tvars, YLabel='Value', title=title, sLabel = sLabel, barSpace = sw)
 
     filename= webqtlUtil.genRandStr("Bar_")
-    c.save(webqtlConfig.IMGDIR+filename, format='gif')
+    c.save(webqtlConfig.GENERATED_IMAGE_DIR+filename, format='gif')
     img=HT.Image('/image/'+filename+'.gif',border=0)
 
     return img
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/maintenance/get_group_samplelists.py b/wqflask/maintenance/get_group_samplelists.py
index b8397b47..a9059fad 100755
--- a/wqflask/maintenance/get_group_samplelists.py
+++ b/wqflask/maintenance/get_group_samplelists.py
@@ -6,7 +6,6 @@ import gzip
 
 from base import webqtlConfig
 
-
 def process_genofiles(geno_dir=webqtlConfig.GENODIR):
     print("Yabba")
     #sys.exit("Dabba")
@@ -54,4 +53,4 @@ def get_samplelist_from_plink(genofilename):
         line = line.split(" ")
         samplelist.append(line[0])
 
-    return samplelist
\ No newline at end of file
+    return samplelist
diff --git a/wqflask/runserver.py b/wqflask/runserver.py
index 59ebf0d4..e4392b3f 100755
--- a/wqflask/runserver.py
+++ b/wqflask/runserver.py
@@ -25,8 +25,8 @@ file_handler = logging.FileHandler(app.config['LOGFILE'])
 file_handler.setLevel(logging.DEBUG)
 app.logger.addHandler(file_handler)
 
-import logging_tree
-logging_tree.printout()
+# import logging_tree
+# logging_tree.printout()
 
 app.run(host='0.0.0.0',
         port=app.config['SERVER_PORT'],
diff --git a/wqflask/utility/external.py b/wqflask/utility/external.py
new file mode 100644
index 00000000..50afea08
--- /dev/null
+++ b/wqflask/utility/external.py
@@ -0,0 +1,9 @@
+# Call external program
+
+import os
+import sys
+import subprocess
+
+def shell(command):
+    if subprocess.call(command, shell=True) != 0:
+        raise Exception("ERROR: failed on "+command)
diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py
new file mode 100644
index 00000000..67b84dc9
--- /dev/null
+++ b/wqflask/utility/genofile_parser.py
@@ -0,0 +1,100 @@
+# CTL analysis for GN2
+# Author / Maintainer: Danny Arends <Danny.Arends@gmail.com>
+
+from __future__ import print_function, division, absolute_import
+import sys
+import os
+import glob
+import traceback
+import gzip
+
+
+import simplejson as json
+
+from pprint import pformat as pf
+
+class Marker(object):
+  def __init__(self):
+    self.name = None
+    self.chr = None
+    self.cM = None
+    self.Mb = None
+    self.genotypes = []
+
+
+class ConvertGenoFile(object):
+
+  def __init__(self, input_file):
+    self.mb_exists = False
+    self.cm_exists = False
+    self.markers = []
+    
+    self.latest_row_pos = None
+    self.latest_col_pos = None
+    
+    self.latest_row_value = None
+    self.latest_col_value = None
+    self.input_fh = open(input_file)
+    print("!!!!!!!!!!!!!!!!PARSER!!!!!!!!!!!!!!!!!!")
+    self.haplotype_notation = {
+      '@mat': "1",
+      '@pat': "2",
+      '@het': "-999",
+      '@unk': "-999"
+    }
+    self.configurations = {}
+
+  def process_rows(self):
+    for self.latest_row_pos, row in enumerate(self.input_fh):
+        self.latest_row_value = row
+        # Take care of headers
+        if not row.strip():
+            continue
+        if row.startswith('#'):
+            continue
+        if row.startswith('Chr'):
+            if 'Mb' in row.split():
+                self.mb_exists = True
+            if 'cM' in row.split():
+                self.cm_exists = True
+            skip = 2 + self.cm_exists + self.mb_exists
+            self.individuals = row.split()[skip:]
+            continue
+        if row.startswith('@'):
+            key, _separater, value = row.partition(':')
+            key = key.strip()
+            value = value.strip()
+            if key in self.haplotype_notation:
+                self.configurations[value] = self.haplotype_notation[key]
+            continue
+        if not len(self.configurations):
+            raise EmptyConfigurations
+        yield row
+
+  def process_csv(self):
+    for row_count, row in enumerate(self.process_rows()):
+      row_items = row.split("\t")
+
+      this_marker = Marker()
+      this_marker.name = row_items[1]
+      this_marker.chr = row_items[0]
+      if self.cm_exists and self.mb_exists:
+        this_marker.cM = row_items[2]
+        this_marker.Mb = row_items[3]
+        genotypes = row_items[4:]
+      elif self.cm_exists:
+          this_marker.cM = row_items[2]
+          genotypes = row_items[3:]
+      elif self.mb_exists:
+          this_marker.Mb = row_items[2]
+          genotypes = row_items[3:]
+      else:
+        genotypes = row_items[2:]
+      for item_count, genotype in enumerate(genotypes):
+        if genotype.upper().strip() in self.configurations:
+          this_marker.genotypes.append(self.configurations[genotype.upper().strip()])
+        else:
+          print("WARNING:", genotype.upper())
+          this_marker.genotypes.append("NA")
+      self.markers.append(this_marker.__dict__)
+
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index b8a41f60..dd8c4a1e 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -1,84 +1,137 @@
 # Tools/paths finder resolves external paths from settings and/or environment
 # variables
-#
-# Currently supported:
-#
-#   PYLMM_PATH finds the root of the git repository of the pylmm_gn2 tool 
 
 import os
 import sys
 from wqflask import app
 
-def get_setting(id,default,guess,get_valid_path):
-    """
-    Resolve a setting from the environment or the global settings in app.config
+def get_setting(command_id,guess=None):
+    """Resolve a setting from the environment or the global settings in
+    app.config, with get_valid_path is a function checking whether the
+    path points to an expected directory and returns the full path to
+    the binary command
+
+      guess = os.environ.get('HOME')+'/pylmm'
+      get_setting('PYLMM_PATH',guess)
+
+    first tries the environment variable in +id+, next gets the Flask
+    app setting for the same +id+ and finally does an educated
+    +guess+.
+
+    In all, the environment overrides the others, next is the flask
+    setting, then the guess. A valid path to the binary command is
+    returned. If none is resolved an exception is thrown.
+
+    Note that we do not use the system path. This is on purpose
+    because it will mess up controlled (reproducible) deployment. The
+    proper way is to either use the GNU Guix defaults as listed in
+    etc/default_settings.py or override them yourself by creating a
+    different settings.py file (or setting the environment).
+
     """
+    def value(command):
+        if command:
+            sys.stderr.write("Found path "+command+"\n")
+            return command
+        else:
+            return None
+    
     # ---- Check whether environment exists
-    path = get_valid_path(os.environ.get(id))
-    # ---- Check whether setting exists
-    setting = app.config.get(id)
-    if not path:
-        path = get_valid_path(setting)
-    # ---- Check whether default exists
-    if not path:
-        path = get_valid_path(default)
-    # ---- Guess directory
-    if not path:
-        if not setting:
-            setting = guess
-        path = get_valid_path(guess)
-    if not path:
-        raise Exception(id+' '+setting+' path unknown or faulty (update settings.py?). '+id+' should point to the root of the git repository')
-
-    return path
-
-def pylmm_command(default=None):
+    sys.stderr.write("Looking for "+command_id+"\n")
+    command = value(os.environ.get(command_id))
+    if not command:
+        # ---- Check whether setting exists in app
+        command = value(app.config.get(command_id))
+        if not command:
+            command = value(guess)
+            if not command:
+                raise Exception(command_id+' path unknown or faulty (update settings.py?). '+command_id+' should point to the path')
+    return command
+
+def valid_bin(bin):
+    if os.path.islink(bin) or valid_file(bin):
+        return bin
+    return None
+
+def valid_file(fn):
+    if os.path.isfile(fn):
+        return fn
+    return None
+
+def valid_path(dir):
+    if os.path.isdir(dir):
+        return dir
+    return None
+
+def pylmm_command(guess=None):
+    return valid_bin(get_setting("PYLMM_COMMAND",guess))
+
+def gemma_command(guess=None):
+    return valid_bin(get_setting("GEMMA_COMMAND",guess))
+
+def plink_command(guess=None):
+    return valid_bin(get_setting("PLINK_COMMAND",guess))
+
+def flat_files(subdir=None):
+    base = get_setting("GENENETWORK_FILES")
+    if subdir:
+        return assert_dir(base+"/"+subdir)
+    return assert_dir(base)
+
+def assert_dir(dir):
+    if not valid_path(dir):
+        raise Exception("ERROR: can not find directory "+dir)
+    return dir
+
+def mk_dir(dir):
+    if not valid_path(dir):
+        os.makedirs(dir)
+    return assert_dir(dir)
+
+def locate(name, subdir=None):
     """
-    Return the path to the repository and the python command to call
+    Locate a static flat file in the GENENETWORK_FILES environment.
+
+    This function throws an error when the file is not found.
     """
-    def get_valid_path(path):
-        """Test for a valid repository"""
-        if path:
-            sys.stderr.write("Trying PYLMM_PATH in "+path+"\n")
-        if path and os.path.isfile(path+'/pylmm_gn2/lmm.py'):
-            return path
+    base = get_setting("GENENETWORK_FILES")
+    if subdir:
+        base = base+"/"+subdir
+    if valid_path(base):
+        lookfor = base + "/" + name
+        if valid_file(lookfor):
+            print("Found: file "+lookfor+"\n")
+            return lookfor
         else:
-            None
+            raise Exception("Can not locate "+lookfor)
+    if subdir: sys.stderr.write(subdir)
+    raise Exception("Can not locate "+name+" in "+base)
 
-    guess = os.environ.get('HOME')+'/pylmm_gn2'
-    path = get_setting('PYLMM_PATH',default,guess,get_valid_path)
-    pylmm_command = 'python '+path+'/pylmm_gn2/lmm.py'
-    return path,pylmm_command
-
-def plink_command(default=None):
+def locate_ignore_error(name, subdir=None):
     """
-    Return the path to the repository and the python command to call
+    Locate a static flat file in the GENENETWORK_FILES environment.
+
+    This function does not throw an error when the file is not found
+    but returns None.
     """
-    def get_valid_path(path):
-        """Test for a valid repository"""
-        if path:
-            sys.stderr.write("Trying PLINK_PATH in "+path+"\n")
-        if path and os.path.isfile(path+'/plink'):
-            return path
-        else:
-            None
-
-    guess = os.environ.get('HOME')+'/plink_gemma'
-    path = get_setting('PLINK_PATH',default,guess,get_valid_path)
-    plink_command = path+'/plink'
-    return path,plink_command
-
-def gemma_command(default=None):
-    def get_valid_path(path):
-        """Test for a valid repository"""
-        if path:
-            sys.stderr.write("Trying PLINK_PATH in "+path+"\n")
-        if path and os.path.isfile(path+'/plink'):
-            return path
-        else:
-            None
+    base = get_setting("GENENETWORK_FILES")
+    if subdir:
+        base = base+"/"+subdir
+    if valid_path(base):
+        lookfor = base + "/" + name
+        if valid_file(lookfor):
+            print("Found: file "+name+"\n")
+            return lookfor
+    sys.stderr.write("WARNING: file "+name+" not found\n")
+    return None
+
+def tempdir():
+    return valid_path(get_setting("TEMPDIR","/tmp"))
 
-    guess = os.environ.get('HOME')+'/plink'
-    path = get_setting('PLINK_PATH',default,guess,get_valid_path)
-    gemma_command = path+'/gemma'
-    return path, gemma_command
\ No newline at end of file
+    
+# Cached values
+PYLMM_COMMAND = pylmm_command()
+GEMMA_COMMAND = gemma_command()
+PLINK_COMMAND = plink_command()
+FLAT_FILES    = flat_files()
+TEMPDIR       = tempdir()
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 98596ca4..dd661092 100755
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -708,13 +708,11 @@ class CorrelationResults(object):
         
         for sample in sample_names:
             if sample not in excluded_samples:
-                value = start_vars['value:' + sample]
-                if value.strip().lower() == 'x':
-                    self.sample_data[str(sample)] = None
-                else:
-                    self.sample_data[str(sample)] = float(value)
-
-
+                # print("Looking for",sample,"in",start_vars)
+                value = start_vars.get('value:' + sample)
+                if value:
+                    if not value.strip().lower() == 'x':
+                        self.sample_data[str(sample)] = float(value)
 
     ##XZ, 12/16/2008: the input geneid is of mouse type
     #def checkForLitInfo(self,geneId):
@@ -942,7 +940,7 @@ class CorrelationResults(object):
                 use_tissue_corr = True
 
             DatabaseFileName = self.getFileName( target_db_name=self.target_db_name )
-            datasetFile = open(webqtlConfig.TEXTDIR+DatabaseFileName,'r')
+            datasetFile = open(webqtlConfig.CACHEDIR+DatabaseFileName,'r')
 
             #XZ, 01/08/2009: read the first line
             line = datasetFile.readline()
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 6bc0ef77..f74e655d 100755
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -43,7 +43,6 @@ from pprint import pformat as pf
 from htmlgen import HTMLgen2 as HT
 import reaper
 
-from base import webqtlConfig
 from utility.THCell import THCell
 from utility.TDCell import TDCell
 from base.trait import GeneralTrait
diff --git a/wqflask/wqflask/ctl/__init__.py b/wqflask/wqflask/ctl/__init__.py
new file mode 100755
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/wqflask/ctl/__init__.py
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py
new file mode 100644
index 00000000..d79d9bfe
--- /dev/null
+++ b/wqflask/wqflask/ctl/ctl_analysis.py
@@ -0,0 +1,194 @@
+# CTL analysis for GN2
+# Author / Maintainer: Danny Arends <Danny.Arends@gmail.com>
+import sys
+from numpy import *
+import scipy as sp                            # SciPy
+import rpy2.robjects as ro                    # R Objects
+import rpy2.rinterface as ri
+
+from base.webqtlConfig import GENERATED_IMAGE_DIR
+from utility import webqtlUtil                # Random number for the image
+from utility import genofile_parser           # genofile_parser
+
+import base64
+import array
+import csv
+import itertools
+
+from base import data_set
+from base import trait as TRAIT
+
+from utility import helper_functions
+from utility.tools import locate
+
+from rpy2.robjects.packages import importr
+utils = importr("utils")
+
+## Get pointers to some common R functions
+r_library       = ro.r["library"]             # Map the library function
+r_options       = ro.r["options"]             # Map the options function
+r_read_csv      = ro.r["read.csv"]            # Map the read.csv function
+r_dim           = ro.r["dim"]                 # Map the dim function
+r_c             = ro.r["c"]                   # Map the c function
+r_t             = ro.r["t"]                   # Map the t function
+r_cat           = ro.r["cat"]                 # Map the cat function
+r_paste         = ro.r["paste"]               # Map the paste function
+r_unlist        = ro.r["unlist"]              # Map the unlist function
+r_head          = ro.r["head"]                # Map the unlist function
+r_unique        = ro.r["unique"]              # Map the unique function
+r_length        = ro.r["length"]              # Map the length function
+r_unlist        = ro.r["unlist"]              # Map the unlist function
+r_list          = ro.r.list                   # Map the list function
+r_matrix        = ro.r.matrix                 # Map the matrix function
+r_seq           = ro.r["seq"]                 # Map the seq function
+r_table         = ro.r["table"]               # Map the table function
+r_names         = ro.r["names"]               # Map the names function
+r_sink          = ro.r["sink"]                # Map the sink function
+r_is_NA         = ro.r["is.na"]               # Map the is.na function
+r_file          = ro.r["file"]                # Map the file function
+r_png           = ro.r["png"]                 # Map the png function for plotting
+r_dev_off       = ro.r["dev.off"]             # Map the dev.off function
+r_save_image    = ro.r["save.image"]          # Map the save.image function
+r_class         = ro.r["class"]               # Map the class function
+r_save          = ro.r["save"]                # Map the save function
+r_write_table   = ro.r["write.table"]         # Map the write.table function
+r_read_table   = ro.r["read.table"]         # Map the read.table function
+r_as_data_frame = ro.r["as.data.frame"]         # Map the write.table function
+r_data_frame    = ro.r["data.frame"]         # Map the write.table function
+r_as_numeric    = ro.r["as.numeric"]         # Map the write.table function
+
+class CTL(object):
+    def __init__(self):
+        print("Initialization of CTL")
+        #log = r_file("/tmp/genenetwork_ctl.log", open = "wt")
+        #r_sink(log)                                  # Uncomment the r_sink() commands to log output from stdout/stderr to a file
+        #r_sink(log, type = "message")
+        r_library("ctl")                                                  # Load CTL - Should only be done once, since it is quite expensive
+        r_options(stringsAsFactors = False)
+        print("Initialization of CTL done, package loaded in R session")
+        self.r_CTLscan            = ro.r["CTLscan"]                        # Map the CTLscan function
+        self.r_CTLsignificant     = ro.r["CTLsignificant"]                 # Map the CTLsignificant function
+        self.r_lineplot           = ro.r["ctl.lineplot"]                   # Map the ctl.lineplot function
+        self.r_CTLsignificant     = ro.r["CTLsignificant"]                 # Map the CTLsignificant function
+        self.r_CTLnetwork         = ro.r["CTLnetwork"]                     # Map the CTLnetwork function
+        self.r_CTLprofiles        = ro.r["CTLprofiles"]                    # Map the CTLprofiles function
+        self.r_plotCTLobject      = ro.r["plot.CTLobject"]                 # Map the CTLsignificant function
+        print("Obtained pointers to CTL functions")
+
+    def run_analysis(self, requestform):
+        print("Starting CTL analysis on dataset")
+        self.trait_db_list = [trait.strip() for trait in requestform['trait_list'].split(',')]
+        self.trait_db_list = [x for x in self.trait_db_list if x]
+
+        print("strategy:", requestform.get("strategy"))
+        strategy = requestform.get("strategy")
+
+        print("nperm:", requestform.get("nperm"))
+        nperm = int(requestform.get("nperm"))
+
+        print("parametric:", requestform.get("parametric"))
+        parametric = bool(requestform.get("parametric"))
+
+        print("significance:", requestform.get("significance"))
+        significance = float(requestform.get("significance"))
+
+        # Get the name of the .geno file belonging to the first phenotype
+        datasetname = self.trait_db_list[0].split(":")[1]
+        dataset = data_set.create_dataset(datasetname)
+
+        genofilelocation = locate(dataset.group.name + ".geno", "genotype")
+        parser = genofile_parser.ConvertGenoFile(genofilelocation)
+        parser.process_csv()
+
+        # Create a genotype matrix
+        individuals = parser.individuals
+        markers = []
+        markernames = []
+        for marker in parser.markers:
+          markernames.append(marker["name"])
+          markers.append(marker["genotypes"])
+
+        genotypes = list(itertools.chain(*markers))
+        print(len(genotypes) / len(individuals), "==", len(parser.markers))
+
+        rGeno = r_t(ro.r.matrix(r_unlist(genotypes), nrow=len(markernames), ncol=len(individuals), dimnames = r_list(markernames, individuals), byrow=True))
+
+        # Create a phenotype matrix
+        traits = []
+        for trait in self.trait_db_list:
+          print("retrieving data for", trait)
+          if trait != "":
+            ts = trait.split(':')
+            gt = TRAIT.GeneralTrait(name = ts[0], dataset_name = ts[1])
+            gt.retrieve_sample_data(individuals)
+            for ind in individuals:
+              if ind in gt.data.keys():
+                traits.append(gt.data[ind].value)
+              else:
+                traits.append("-999")
+
+        rPheno = r_t(ro.r.matrix(r_as_numeric(r_unlist(traits)), nrow=len(self.trait_db_list), ncol=len(individuals), dimnames = r_list(self.trait_db_list, individuals), byrow=True))
+
+        # Use a data frame to store the objects
+        rPheno = r_data_frame(rPheno)
+        rGeno = r_data_frame(rGeno)
+
+        # Debug: Print the genotype and phenotype files to disk
+        #r_write_table(rGeno, "~/outputGN/geno.csv")
+        #r_write_table(rPheno, "~/outputGN/pheno.csv")
+
+        # Perform the CTL scan
+        res = self.r_CTLscan(rGeno, rPheno, strategy = strategy, nperm = nperm, parametric = parametric, ncores = 6)
+
+        # Get significant interactions
+        significant = self.r_CTLsignificant(res, significance = significance)
+
+        # Create an image for output
+        self.results = {}
+        self.results['imgurl1'] = webqtlUtil.genRandStr("CTLline_") + ".png"
+        self.results['imgloc1'] = GENERATED_IMAGE_DIR + self.results['imgurl1']
+
+        self.results['ctlresult'] = significant
+        self.results['requestform'] = requestform             # Store the user specified parameters for the output page
+
+        # Create the lineplot
+        r_png(self.results['imgloc1'], width=1000, height=600)
+        self.r_lineplot(res, significance = significance)
+        r_dev_off()
+
+        n = 2
+        for trait in self.trait_db_list:
+          # Create the QTL like CTL plots
+          self.results['imgurl' + str(n)] = webqtlUtil.genRandStr("CTL_") + ".png"
+          self.results['imgloc' + str(n)] = GENERATED_IMAGE_DIR + self.results['imgurl' + str(n)]
+          r_png(self.results['imgloc' + str(n)], width=1000, height=600)
+          self.r_plotCTLobject(res, (n-1), significance = significance, main='Phenotype ' + trait)
+          r_dev_off()
+          n = n + 1
+
+        # Flush any output from R
+        sys.stdout.flush()
+
+    def loadImage(self, path, name):
+        print("pre-loading imgage results:", self.results[path])
+        imgfile = open(self.results[path], 'rb')
+        imgdata = imgfile.read()
+        imgB64 = imgdata.encode("base64")
+        bytesarray = array.array('B', imgB64)
+        self.results[name] = bytesarray
+
+    def render_image(self, results):
+        self.loadImage("imgloc1", "imgdata1")
+        n = 2
+        for trait in self.trait_db_list:
+          self.loadImage("imgloc" + str(n), "imgdata" + str(n))
+          n = n + 1
+
+    def process_results(self, results):
+        print("Processing CTL output")
+        template_vars = {}
+        template_vars["results"] = self.results
+        self.render_image(self.results)
+        sys.stdout.flush()
+        return(dict(template_vars))
+
diff --git a/wqflask/wqflask/database.py b/wqflask/wqflask/database.py
index 159c5d6c..2f544d44 100755
--- a/wqflask/wqflask/database.py
+++ b/wqflask/wqflask/database.py
@@ -24,8 +24,9 @@ def init_db():
     # you will have to import them first before calling init_db()
     #import yourapplication.models
     import wqflask.model
-    print("Creating all..")
+    print("database.py: Creating all model metadata..")
     Base.metadata.create_all(bind=engine)
-    print("Done creating all...")
+    print("database.py: Done creating all model metadata...")
+    print("Point your browser at http://localhost:5003/")
     
 init_db()
diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py
index 40f518f0..2445b37f 100644
--- a/wqflask/wqflask/heatmap/heatmap.py
+++ b/wqflask/wqflask/heatmap/heatmap.py
@@ -26,13 +26,12 @@ import reaper
 from base.trait import GeneralTrait
 from base import data_set
 from base import species
-from base import webqtlConfig
-from utility import webqtlUtil
 # from wqflask.my_pylmm.pyLMM import lmm
 # from wqflask.my_pylmm.pyLMM import input
 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
 
@@ -214,7 +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")
@@ -273,7 +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/interval_analyst/IntervalAnalystPage.py b/wqflask/wqflask/interval_analyst/IntervalAnalystPage.py
index ec9aa29c..f45ec0c4 100755
--- a/wqflask/wqflask/interval_analyst/IntervalAnalystPage.py
+++ b/wqflask/wqflask/interval_analyst/IntervalAnalystPage.py
@@ -45,40 +45,40 @@ class IntervalAnalystPage(templatePage):
 	#A dictionary that lets us map the html form names "txStart_mm6" -> "Mb Start (mm8)"
 	#the first item is the short name (column headers) and the second item is the long name (dropdown list)
 	#   [short name, long name, category]
-	columnNames = {"GeneSymbol" : ["Gene", "Gene Name", 'gene'], 
+	columnNames = {"GeneSymbol" : ["Gene", "Gene Name", 'gene'],
 			"GeneDescription" : ["Description", "Gene Description", 'species'],
-			'GeneNeighborsCount' : ["Neighbors", "Gene Neighbors", 'gene'], 
-			'GeneNeighborsRange' : ["Neighborhood", "Gene Neighborhood (Mb)", 'gene'], 
-			'GeneNeighborsDensity' : ["Gene Density", "Gene Density (Neighbors/Mb)", 'gene'],  
+			'GeneNeighborsCount' : ["Neighbors", "Gene Neighbors", 'gene'],
+			'GeneNeighborsRange' : ["Neighborhood", "Gene Neighborhood (Mb)", 'gene'],
+			'GeneNeighborsDensity' : ["Gene Density", "Gene Density (Neighbors/Mb)", 'gene'],
 			"ProteinID" : ["Prot ID", "Protein ID", 'protein'],
-			"Chromosome" : ["Chr", "Chromosome", 'species'], 
-			"TxStart" : ["Start", "Mb Start", 'species'], 
-			"TxEnd" : ["End", "Mb End", 'species'], 
-			"GeneLength" : ["Length", "Kb Length", 'species'], 
-			"cdsStart" : ["CDS Start", "Mb CDS Start", 'species'], 
+			"Chromosome" : ["Chr", "Chromosome", 'species'],
+			"TxStart" : ["Start", "Mb Start", 'species'],
+			"TxEnd" : ["End", "Mb End", 'species'],
+			"GeneLength" : ["Length", "Kb Length", 'species'],
+			"cdsStart" : ["CDS Start", "Mb CDS Start", 'species'],
 			"cdsEnd" : ["CDS End", "Mb CDS End", 'species'],
-			"exonCount" : ["Num Exons", "Exon Count", 'species'], 
-			"exonStarts" : ["Exon Starts", "Exon Starts", 'species'], 
-			"exonEnds" : ["Exon Ends", "Exon Ends", 'species'], 
-			"Strand" : ["Strand", "Strand", 'species'], 
+			"exonCount" : ["Num Exons", "Exon Count", 'species'],
+			"exonStarts" : ["Exon Starts", "Exon Starts", 'species'],
+			"exonEnds" : ["Exon Ends", "Exon Ends", 'species'],
+			"Strand" : ["Strand", "Strand", 'species'],
 			"GeneID" : ["Gene ID", "Gene ID", 'species'],
-			"GenBankID" : ["GenBank", "GenBank ID", 'species'], 
+			"GenBankID" : ["GenBank", "GenBank ID", 'species'],
 			"UnigenID" : ["Unigen", "Unigen ID", 'species'],
-			"NM_ID" : ["NM ID", "NM ID", 'species'], 
+			"NM_ID" : ["NM ID", "NM ID", 'species'],
 			"kgID" : ["kg ID", "kg ID", 'species'],
-			"snpCount" : ["SNPs", "SNP Count", 'species'], 
-			"snpDensity" : ["SNP Density", "SNP Density", 'species'], 
-			"lrs" : ["LRS", "Likelihood Ratio Statistic", 'misc'], 
-			"lod" : ["LOD", "Likelihood Odds Ratio", 'misc'], 
-			"pearson" : ["Pearson", "Pearson Product Moment", 'misc'], 
-			"literature" : ["Lit Corr", "Literature Correlation", 'misc'], 
+			"snpCount" : ["SNPs", "SNP Count", 'species'],
+			"snpDensity" : ["SNP Density", "SNP Density", 'species'],
+			"lrs" : ["LRS", "Likelihood Ratio Statistic", 'misc'],
+			"lod" : ["LOD", "Likelihood Odds Ratio", 'misc'],
+			"pearson" : ["Pearson", "Pearson Product Moment", 'misc'],
+			"literature" : ["Lit Corr", "Literature Correlation", 'misc'],
 			}
 
 	###Species Freeze
 	speciesFreeze = {'mouse':'mm9', 'rat':'rn3', 'human':'hg19'}
 	for key in speciesFreeze.keys():
 		speciesFreeze[speciesFreeze[key]] = key
-	
+
 	def __init__(self, fd):
 
 		templatePage.__init__(self, fd)
@@ -86,7 +86,7 @@ class IntervalAnalystPage(templatePage):
 		fd.formdata['remote_ip'] = fd.remote_ip
 		if not self.openMysql():
 			return
-		
+
 		self.species = fd.formdata.getvalue("species", "mouse")
 		try:
 			self.startMb = float(fd.formdata.getvalue("startMb"))
@@ -96,7 +96,7 @@ class IntervalAnalystPage(templatePage):
 			self.endMb = float(fd.formdata.getvalue("endMb"))
 		except:
 			self.endMb = self.startMb + 10
-			
+
 		self.Chr = fd.formdata.getvalue("chromosome", "1")
 		self.xls = fd.formdata.getvalue("xls", "1")
 		try:
@@ -107,38 +107,38 @@ class IntervalAnalystPage(templatePage):
 			self.diffColDefault = self.diffCol = []
 			if self.species !=  'mouse':
 				self.diffColDefault = [2, 3]#default is B6 and D2 for other species
-			
+
 		controlFrm, dispFields = self.genControlForm(fd)
 		geneTable, filename = self.genGeneTable(fd, dispFields)
-		
+
 		infoTD = HT.TD(width=400, valign= "top")
-		infoTD.append(HT.Paragraph("Interval Analyst : Chr %s" % self.Chr, Class="title"), 
-			HT.Strong("Species : "), self.species.title(), HT.BR(),  
-			HT.Strong("Database : "), "UCSC %s" % self.speciesFreeze[self.species], HT.BR(),  
-			HT.Strong("Range : "), "%2.6f Mb - %2.6f Mb" % (self.startMb, self.endMb), HT.BR(),  
+		infoTD.append(HT.Paragraph("Interval Analyst : Chr %s" % self.Chr, Class="title"),
+			HT.Strong("Species : "), self.species.title(), HT.BR(),
+			HT.Strong("Database : "), "UCSC %s" % self.speciesFreeze[self.species], HT.BR(),
+			HT.Strong("Range : "), "%2.6f Mb - %2.6f Mb" % (self.startMb, self.endMb), HT.BR(),
 			)
 		if filename:
 			infoTD.append(HT.BR(), HT.BR(), HT.Href(text="Download", url = "/tmp/" + filename, Class="normalsize")
 					, " output in MS excel format.")
-		
+
 		mainTable = HT.TableLite(HT.TR(infoTD, HT.TD(controlFrm, Class="doubleBorder", width=400), HT.TD("&nbsp;", width="")), cellpadding=10)
 		mainTable.append(HT.TR(HT.TD(geneTable, colspan=3)))
 		self.dict['body'] = HT.TD(mainTable)
 		self.dict['title'] = "Interval Analyst"
-		
+
 	def genGeneTable(self, fd, dispFields):
 		filename = ""
 		if self.xls:
 			#import pyXLWriter as xl
 			filename = "IntAn_Chr%s_%2.6f-%2.6f" % (self.Chr, self.startMb, self.endMb)
 			filename += ".xls"
-			
+
 			# Create a new Excel workbook
 			workbook = xl.Writer(os.path.join(webqtlConfig.TMPDIR, filename))
 			worksheet = workbook.add_worksheet()
 			titleStyle = workbook.add_format(align = 'left', bold = 0, size=18, border = 1, border_color="gray")
 			headingStyle = workbook.add_format(align = 'center', bold = 1, size=13, fg_color = 0x1E, color="white", border = 1, border_color="gray")
-			
+
 			##Write title Info
 			worksheet.write([0, 0], "GeneNetwork Interval Analyst Table", titleStyle)
 			worksheet.write([1, 0], "%s%s" % (webqtlConfig.PORTADDR, os.path.join(webqtlConfig.CGIDIR, self._scriptfile)))
@@ -148,12 +148,12 @@ class IntervalAnalystPage(templatePage):
 			worksheet.write([4, 0], "Search by : %s" % fd.formdata['remote_ip'])
 			worksheet.write([5, 0], "view region : Chr %s %2.6f - %2.6f Mb" % (self.Chr, self.startMb, self.endMb))
 			nTitleRow = 7
-			
+
 		geneTable = HT.TableLite(Class="collap", cellpadding=5)
 		headerRow = HT.TR(HT.TD(" ", Class="fs13 fwb ffl b1 cw cbrb", width="1"))
 		if self.xls:
 			worksheet.write([nTitleRow, 0], "Index", headingStyle)
-			
+
 		for ncol, column in enumerate(dispFields):
 			if len(column) == 1:
 				headerRow.append(HT.TD(self.columnNames[column[0]][0], Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1,align="Center"))
@@ -162,24 +162,24 @@ class IntervalAnalystPage(templatePage):
 					worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle)
 					worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle))
 			else:
-				headerRow.append(HT.TD(self.columnNames[column[0]][0], HT.BR(), " (%s)" % self.speciesFreeze[column[1]], 
+				headerRow.append(HT.TD(self.columnNames[column[0]][0], HT.BR(), " (%s)" % self.speciesFreeze[column[1]],
 					Class="fs13 fwb ffl b1 cw cbrb", NOWRAP=1, align="Center"))
 				if self.xls:
 					colTitle = self.columnNames[column[0]][0] + " (%s)" % self.speciesFreeze[column[1]]
 					worksheet.write([nTitleRow, ncol+1], colTitle, headingStyle)
 					worksheet.set_column([ncol+1, ncol+1], 2*len(colTitle))
-				#headerRow.append(HT.TD(self.columnNames[column[0]][0], HT.BR(), 
-				#	"(%s %s)" % (column[1].title(), self.speciesFreeze[column[1]]), 
+				#headerRow.append(HT.TD(self.columnNames[column[0]][0], HT.BR(),
+				#	"(%s %s)" % (column[1].title(), self.speciesFreeze[column[1]]),
 				#	Class="colorBlue", NOWRAP=1, align="Center"))
 		geneTable.append(headerRow)
-		
+
 		geneCol = GeneUtil.loadGenes(self.cursor, self.Chr, self.diffColDefault, self.startMb, self.endMb, species=self.species)
 		for gIndex, theGO in enumerate(geneCol):
 			geneRow = HT.TR(HT.TD(gIndex+1, Class="fs12 fwn b1", align="right"))
 			if self.xls:
 				nTitleRow += 1
 				worksheet.write([nTitleRow, 0], gIndex + 1)
-				
+
 			for ncol, column in enumerate(dispFields):
 				if len(column) == 1 or column[1]== self.species:
 					keyValue = ""
@@ -196,17 +196,17 @@ class IntervalAnalystPage(templatePage):
 					curGO = theGO[subGO]
 					if theGO[subGO].has_key(fieldName):
 						keyValue = theGO[subGO][fieldName]
-				
+
 				if self.xls:
 					worksheet.write([nTitleRow, ncol+1], keyValue)
 				geneRow.append(self.formatTD(keyValue, fieldName, curSpecies, curGO))
-					
+
 			geneTable.append(geneRow)
-			
+
 		if self.xls:
 			workbook.close()
 		return geneTable, filename
-	
+
 	def formatTD(self, keyValue, fieldName, Species, theGO):
 		if keyValue is None:
 			keyValue = ""
@@ -219,7 +219,7 @@ class IntervalAnalystPage(templatePage):
 					keyValue = ""
 				return HT.TD(keyValue, Class="fs12 fwn b1", width=300)
 			elif fieldName in ("GeneSymbol"):
-				webqtlLink = HT.Href("./%s?cmd=sch&gene=%s&alias=1&species=%s" % (webqtlConfig.SCRIPTFILE, keyValue, Species), 		
+				webqtlLink = HT.Href("./%s?cmd=sch&gene=%s&alias=1&species=%s" % (webqtlConfig.SCRIPTFILE, keyValue, Species), 
 					HT.Image("/images/webqtl_search.gif", border=0, valign="top"), target="_blank")
 				if theGO['GeneID']:
 					geneSymbolLink = HT.Href(webqtlConfig.NCBI_LOCUSID % theGO['GeneID'], keyValue, Class="normalsize", target="_blank")
@@ -236,8 +236,8 @@ class IntervalAnalystPage(templatePage):
 				return HT.TD(keyValue, Class="fs12 fwn b1",align="right")
 			elif fieldName in ("snpCount"):
 				if keyValue:
-					snpString = HT.Href(url="%s&chr=%s&start=%s&end=%s&geneName=%s&s1=%d&s2=%d" % (os.path.join(webqtlConfig.CGIDIR, 'main.py?FormID=snpBrowser'), 
-							theGO["Chromosome"], theGO["TxStart"], theGO["TxEnd"], theGO["GeneSymbol"], self.diffColDefault[0], self.diffColDefault[1]), 
+					snpString = HT.Href(url="%s&chr=%s&start=%s&end=%s&geneName=%s&s1=%d&s2=%d" % (os.path.join(webqtlConfig.CGIDIR, 'main.py?FormID=snpBrowser'),
+							theGO["Chromosome"], theGO["TxStart"], theGO["TxEnd"], theGO["GeneSymbol"], self.diffColDefault[0], self.diffColDefault[1]),
 							text=theGO["snpCount"], target="_blank", Class="normalsize")
 				else:
 					snpString = keyValue
@@ -252,13 +252,13 @@ class IntervalAnalystPage(templatePage):
 				return HT.TD(keyValue, Class="fs12 fwn b1",NOWRAP=1)
 		else:
 			return HT.TD(keyValue, Class="fs12 fwn b1",NOWRAP=1,align="right")
-				
+
 	def genControlForm(self, fd):
 		##desc GeneList
 		self.cursor.execute("Desc GeneList")
 		GeneListFields = self.cursor.fetchall()
 		GeneListFields = map(lambda X: X[0], GeneListFields)
-		
+
 		#group columns by category--used for creating the dropdown list of possible columns
 		categories = {}
 		for item in self.columnNames.keys():
@@ -267,7 +267,7 @@ class IntervalAnalystPage(templatePage):
 				categories[category[-1]] = [item ]
 			else:
 				categories[category[-1]] = categories[category[-1]]+[item]
-	
+
 		##List All Species in the Gene Table
 		speciesDict = {}
 		self.cursor.execute("select Species.Name, GeneList.SpeciesId from Species, GeneList where \
@@ -292,34 +292,34 @@ class IntervalAnalystPage(templatePage):
 					pass
 				AppliedField.append(item2)
 			categories[specName] = AppliedField
-			
+
 		categoriesOrder += ['misc']
-		
+
 		############################################################
 		## Create the list of possible columns for the dropdown list
 		############################################################
 		allColumnsList = HT.Select(name="allColumns", Class="snpBrowserDropBox")
-		
+
 		for category in categoriesOrder:
 			allFields = categories[category]
 			if allFields:
 				geneOpt = HT.Optgroup(label=category.title())
 				for item in allFields:
 					if category in self.speciesFreeze.keys():
-						geneOpt.append(("%s (%s %s)" % (self.columnNames[item][1], category.title(), self.speciesFreeze[category]), 
+						geneOpt.append(("%s (%s %s)" % (self.columnNames[item][1], category.title(), self.speciesFreeze[category]),
 							"%s__%s" % (item, self.speciesFreeze[category])))
 					else:
 						geneOpt.append((self.columnNames[item][1], item))
 				geneOpt.sort()
 				allColumnsList.append(geneOpt)
-		
+
 		######################################
 		## Create the list of selected columns
 		######################################
-		
+
 		#cols contains the value of all the selected columns
 		submitCols = cols = fd.formdata.getvalue("columns", "default")
-		
+
 		if cols == "default":
 			if self.species=="mouse":  #these are the same columns that are shown on intervalPage.py
 				cols = ['GeneSymbol', 'GeneDescription', 'Chromosome', 'TxStart', 'Strand', 'GeneLength', 'GeneID', 'NM_ID', 'snpCount', 'snpDensity']
@@ -331,12 +331,12 @@ class IntervalAnalystPage(templatePage):
 		else:
 			if type(cols)==type(""):
 				cols = [cols]
-			
+
 		colsLst = []
 		dispFields = []
 		for column in cols:
 			if submitCols == "default" and column not in ('GeneSymbol') and (column in GeneListFields or column in speciesField):
-				colsLst.append(("%s (%s %s)" % (self.columnNames[column][1], self.species.title(), self.speciesFreeze[self.species]), 
+				colsLst.append(("%s (%s %s)" % (self.columnNames[column][1], self.species.title(), self.speciesFreeze[self.species]),
 							"%s__%s" % (column, self.speciesFreeze[self.species])))
 				dispFields.append([column, self.species])
 			else:
@@ -346,17 +346,17 @@ class IntervalAnalystPage(templatePage):
 					dispFields.append([column])
 				else:
 					thisSpecies = self.speciesFreeze[column2[1]]
-					colsLst.append(("%s (%s %s)" % (self.columnNames[column2[0]][1], thisSpecies.title(), column2[1]), 
+					colsLst.append(("%s (%s %s)" % (self.columnNames[column2[0]][1], thisSpecies.title(), column2[1]),
 							column))
 					dispFields.append((column2[0], thisSpecies))
 		selectedColumnsList = HT.Select(name="columns", Class="snpBrowserSelectBox", multiple="true", data=colsLst, size=6)
-		
+
 		##########################
         ## Create the columns form
-		##########################		
+		##########################
 		columnsForm = HT.Form(name="columnsForm", submit=HT.Input(type='hidden'), cgi=os.path.join(webqtlConfig.CGIDIR, self._scriptfile), enctype="multipart/form-data")
 		columnsForm.append(HT.Input(type="hidden", name="fromdatabase", value= fd.formdata.getvalue("fromdatabase", "unknown")))
-		columnsForm.append(HT.Input(type="hidden", name="species", value=self.species))	
+		columnsForm.append(HT.Input(type="hidden", name="species", value=self.species))
 		if self.diffCol:
 			columnsForm.append(HT.Input(type="hidden", name="s1", value=self.diffCol[0]))
 			columnsForm.append(HT.Input(type="hidden", name="s2", value=self.diffCol[1]))
@@ -366,8 +366,8 @@ class IntervalAnalystPage(templatePage):
 		removeButton = HT.Input(type="button", name="remove", value="Remove", Class="button", onClick="removeFromList(this.form.columns.selectedIndex, this.form.columns)")
 		upButton = HT.Input(type="button", name="up", value="Up", Class="button", onClick="swapOptions(this.form.columns.selectedIndex, this.form.columns.selectedIndex-1, this.form.columns)")
 		downButton = HT.Input(type="button", name="down", value="Down", Class="button", onClick="swapOptions(this.form.columns.selectedIndex, this.form.columns.selectedIndex+1, this.form.columns)")
-		clearButton = HT.Input(type="button", name="clear", value="Clear", Class="button", onClick="deleteAllElements(this.form.columns)")		
-		submitButton = HT.Input(type="submit", value="Refresh", Class="button", onClick="selectAllElements(this.form.columns)")		
+		clearButton = HT.Input(type="button", name="clear", value="Clear", Class="button", onClick="deleteAllElements(this.form.columns)")
+		submitButton = HT.Input(type="submit", value="Refresh", Class="button", onClick="selectAllElements(this.form.columns)")
 
 		selectChrBox = HT.Select(name="chromosome")
 		self.cursor.execute("""
@@ -375,11 +375,11 @@ class IntervalAnalystPage(templatePage):
 				Chr_Length.Name, Length from Chr_Length, Species
 			where
 				Chr_Length.SpeciesId = Species.Id AND
-				Species.Name = '%s' 
+				Species.Name = '%s'
 			Order by
 				Chr_Length.OrderId
 			""" % self.species)
-		
+
 		results = self.cursor.fetchall()
 		for chrInfo in results:
 			selectChrBox.append((chrInfo[0], chrInfo[0]))
@@ -401,5 +401,5 @@ class IntervalAnalystPage(templatePage):
 		#columnsForm.append(HT.Input(type="hidden", name="sort", value=diffCol),
 		#		   HT.Input(type="hidden", name="identification", value=identification),
 		#		   HT.Input(type="hidden", name="traitInfo", value=traitInfo))
-		
+
 		return columnsForm, dispFields
diff --git a/wqflask/wqflask/marker_regression/MarkerRegressionPage.py b/wqflask/wqflask/marker_regression/MarkerRegressionPage.py
index d02d80b3..455fcf95 100755
--- a/wqflask/wqflask/marker_regression/MarkerRegressionPage.py
+++ b/wqflask/wqflask/marker_regression/MarkerRegressionPage.py
@@ -140,7 +140,7 @@ class MarkerRegressionPage(templatePage):
                 intCanvas = pid.PILCanvas(size=(self.graphWidth,self.graphHeight))
                 gifmap = self.plotIntMappingForPLINK(fd, intCanvas, startMb = self.startMb, endMb = self.endMb, plinkResultDict=plinkResultDict)
 
-                intCanvas.save(os.path.join(webqtlConfig.IMGDIR, filename), format='png')
+                intCanvas.save(os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, filename), format='png')
                 intImg=HT.Image('/image/'+filename+'.png', border=0, usemap='#WebQTLImageMap')
 
                 TD_LR = HT.TR(HT.TD(HT.Blockquote(gifmap,intImg, HT.P()), bgColor='#eeeeee', height = 200))
@@ -249,7 +249,7 @@ class MarkerRegressionPage(templatePage):
                 intCanvas = pid.PILCanvas(size=(self.graphWidth,self.graphHeight))
                 gifmap = self.plotIntMapping(fd, intCanvas, startMb = self.startMb, endMb = self.endMb, showLocusForm= "")
                 filename= webqtlUtil.genRandStr("Itvl_")
-                intCanvas.save(os.path.join(webqtlConfig.IMGDIR, filename), format='png')
+                intCanvas.save(os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, filename), format='png')
                 intImg=HT.Image('/image/'+filename+'.png', border=0, usemap='#WebQTLImageMap')
 
                 ################################################################
@@ -458,7 +458,7 @@ class MarkerRegressionPage(templatePage):
         #plotBar(myCanvas,10,10,390,290,LRSArray,XLabel='LRS',YLabel='Frequency',title=' Histogram of Permutation Test',identification=fd.identification)
         Plot.plotBar(myCanvas, LRSArray,XLabel='LRS',YLabel='Frequency',title=' Histogram of Permutation Test')
         filename= webqtlUtil.genRandStr("Reg_")
-        myCanvas.save(webqtlConfig.IMGDIR+filename, format='gif')
+        myCanvas.save(webqtlConfig.GENERATED_IMAGE_DIR+filename, format='gif')
         img=HT.Image('/image/'+filename+'.gif',border=0,alt='Histogram of Permutation Test')
             
         if fd.suggestive == None:
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index cfcd4783..8fb086c1 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -1,9 +1,7 @@
 import os
 
 from base import webqtlConfig
-from utility.tools import gemma_command
-
-GEMMA_PATH,GEMMA_COMMAND = gemma_command()
+from utility.tools import GEMMA_COMMAND
 
 def run_gemma(this_dataset, samples, vals): 
     """Generates p-values for each marker using GEMMA"""
@@ -12,8 +10,11 @@ def run_gemma(this_dataset, samples, vals):
 
     gen_pheno_txt_file(this_dataset, samples, vals)
 
-    os.chdir(GEMMA_PATH)
+    # Don't do this!
+    # os.chdir("{}gemma".format(webqtlConfig.HTMLPATH))
 
+    # use GEMMA_RUN in the next one, create a unique temp file
+    
     gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/output/%s.cXX.txt -lmm 1 -o %s_output' % (GEMMA_PATH,
                                                                                     this_dataset.group.name,
                                                                                     GEMMA_PATH,
@@ -46,4 +47,4 @@ def parse_gemma_output(this_dataset):
                 p_values.append(float(line.split("\t")[10]))
 
     #print("p_values: ", p_values)
-    return included_markers, p_values
\ No newline at end of file
+    return included_markers, p_values
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index fa439b55..b56b179b 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -30,21 +30,16 @@ from flask import Flask, g
 from base.trait import GeneralTrait
 from base import data_set
 from base import species
-from base import webqtlConfig
 from utility import webqtlUtil
 from utility import helper_functions
 from utility import Plot, Bunch
 from utility import temp_data
 from utility.benchmark import Bench
-from utility.tools import pylmm_command, plink_command, gemma_command
 from wqflask.marker_regression import gemma_mapping
-#from wqflask.marker_regression import qtl_reaper_mapping
-#from wqflask.marker_regression import plink_mapping
-#from wqflask.marker_regression import rqtl_mapping
 
-PYLMM_PATH,PYLMM_COMMAND = pylmm_command()
-PLINK_PATH,PLINK_COMMAND = plink_command()
-GEMMA_PATH,GEMMA_COMMAND = gemma_command()
+from utility.tools import locate, locate_ignore_error, PYLMM_COMMAND, GEMMA_COMMAND, PLINK_COMMAND
+from utility.external import shell
+from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR
 
 class MarkerRegression(object):
 
@@ -299,22 +294,14 @@ class MarkerRegression(object):
         included_markers, p_values = self.parse_gemma_output()
         
         self.dataset.group.get_specified_markers(markers = included_markers)
-        
-        #for marker in self.dataset.group.markers.markers:
-        #    if marker['name'] not in included_markers:
-        #        print("marker:", marker)
-        #        self.dataset.group.markers.markers.remove(marker)
-        #        #del self.dataset.group.markers.markers[marker]
-        
         self.dataset.group.markers.add_pvalues(p_values)
-
         return self.dataset.group.markers.markers
 
-
     def parse_gemma_output(self):
         included_markers = []
         p_values = []
-        with open("/home/zas1024/gene/web/gemma/output/{}_output.assoc.txt".format(self.dataset.group.name)) as output_file:
+        # Use a temporary file name here!
+        with open(webqtlConfig.GENERATED_TEXT_DIR+"/{}_output.assoc.txt".format(self.dataset.group.name)) as output_file:
             for line in output_file:
                 if line.startswith("chr"):
                     continue
@@ -327,37 +314,18 @@ class MarkerRegression(object):
 
     def gen_pheno_txt_file(self):
         """Generates phenotype file for GEMMA"""
-        
-        #with open("/home/zas1024/gene/web/gemma/tmp_pheno/{}.txt".format(filename), "w") as outfile:
-        #    for sample, i in enumerate(self.samples):
-        #        print("sample:" + str(i))
-        #        print("self.vals[i]:" + str(self.vals[sample]))
-        #        outfile.write(str(i) + "\t" + str(self.vals[sample]) + "\n")
-                
-        with open("/home/zas1024/gene/web/gemma/{}.fam".format(self.dataset.group.name), "w") as outfile:
+        with open(webqtlConfig.GENERATED_TEXT_DIR+"{}.fam".format(self.dataset.group.name), "w") as outfile:
             for i, sample in enumerate(self.samples):
                 outfile.write(str(sample) + " " + str(sample) + " 0 0 0 " + str(self.vals[i]) + "\n")
-
-    #def gen_plink_for_gemma(self, filename):
-    #    
-    #    make_bed = "/home/zas1024/plink/plink --file /home/zas1024/plink/%s --noweb --no-fid --no-parents --no-sex --no-pheno --pheno %s%s.txt --out %s%s --make-bed" % (webqtlConfig.HTMLPATH,
-    #                                                                                                                                             webqtlConfig.HTMLPATH,
-    #                                                                                                                                             self.dataset.group.name,
-    #                                                                                                                                             webqtlConfig.TMPDIR,
-    #                                                                                                                                             filename,
-    #                                                                                                                                             webqtlConfig.TMPDIR,
-    #                                                                                                                                             filename)
-    #
-    #
     
     def run_rqtl_plink(self):
-        os.chdir("/home/zas1024/plink")
+        # os.chdir("") never do this inside a webserver!!
         
         output_filename = webqtlUtil.genRandStr("%s_%s_"%(self.dataset.group.name, self.this_trait.name))
         
         self.gen_pheno_txt_file_plink(pheno_filename = output_filename)
         
-        rqtl_command = './plink --noweb --ped %s.ped --no-fid --no-parents --no-sex --no-pheno --map %s.map --pheno %s/%s.txt --pheno-name %s --maf %s --missing-phenotype -9999 --out %s%s --assoc ' % (self.dataset.group.name, self.dataset.group.name, webqtlConfig.TMPDIR, plink_output_filename, self.this_trait.name, self.maf, webqtlConfig.TMPDIR, plink_output_filename)
+        rqtl_command = './plink --noweb --ped %s.ped --no-fid --no-parents --no-sex --no-pheno --map %s.map --pheno %s/%s.txt --pheno-name %s --maf %s --missing-phenotype -9999 --out %s%s --assoc ' % (self.dataset.group.name, self.dataset.group.name, TMPDIR, plink_output_filename, self.this_trait.name, self.maf, TMPDIR, plink_output_filename)
         
         os.system(rqtl_command)
         
@@ -414,10 +382,11 @@ class MarkerRegression(object):
         calc_genoprob   = ro.r["calc.genoprob"]         # Map the calc.genoprob function
         read_cross      = ro.r["read.cross"]            # Map the read.cross function
         write_cross     = ro.r["write.cross"]           # Map the write.cross function
-        GENOtoCSVR      = ro.r["GENOtoCSVR"]            # Map the GENOtoCSVR function
+        GENOtoCSVR      = ro.r["GENOtoCSVR"]            # Map the local GENOtoCSVR function
 
-        genofilelocation  = webqtlConfig.HTMLPATH + "genotypes/" + self.dataset.group.name + ".geno"
-        crossfilelocation = webqtlConfig.HTMLPATH + "genotypes/" + self.dataset.group.name + ".cross"
+        crossname = self.dataset.group.name
+        genofilelocation  = locate(crossname + ".geno", "genotype")
+        crossfilelocation = TMPDIR + crossname + ".cross"
 
         #print("Conversion of geno to cross at location:", genofilelocation, " to ", crossfilelocation)
 
@@ -444,7 +413,7 @@ class MarkerRegression(object):
             #print("Pair scan results:", result_data_frame)
 
             self.pair_scan_filename = webqtlUtil.genRandStr("scantwo_") + ".png"
-            png(file=webqtlConfig.TMPDIR+self.pair_scan_filename)
+            png(file=TMPDIR+self.pair_scan_filename)
             plot(result_data_frame)
             dev_off()
             
@@ -554,8 +523,8 @@ class MarkerRegression(object):
         
         self.gen_pheno_txt_file_plink(pheno_filename = plink_output_filename)
         
-        plink_command = PLINK_COMMAND + ' --noweb --bed %s/%s.bed --bim %s/%s.bim --fam %s/%s.fam --no-fid --no-parents --no-sex --no-pheno --pheno %s%s.txt --pheno-name %s --maf %s --missing-phenotype -9999 --out %s%s --assoc ' % (PLINK_PATH, self.dataset.group.name, PLINK_PATH, self.dataset.group.name, PLINK_PATH, self.dataset.group.name, webqtlConfig.TMPDIR, plink_output_filename, self.this_trait.name, self.maf, webqtlConfig.TMPDIR, plink_output_filename)
-        #print("plink_command:", plink_command)        
+        plink_command = PLINK_COMMAND + ' --noweb --ped %s/%s.ped --no-fid --no-parents --no-sex --no-pheno --map %s/%s.map --pheno %s%s.txt --pheno-name %s --maf %s --missing-phenotype -9999 --out %s%s --assoc ' % (PLINK_PATH, self.dataset.group.name, PLINK_PATH, self.dataset.group.name, TMPDIR, plink_output_filename, self.this_trait.name, self.maf, TMPDIR, plink_output_filename)
+        print("plink_command:", plink_command)        
 
         os.system(plink_command)
 
@@ -576,7 +545,7 @@ class MarkerRegression(object):
 
     def gen_pheno_txt_file_plink(self, pheno_filename = ''):
         ped_sample_list = self.get_samples_from_ped_file()	
-        output_file = open("%s%s.txt" % (webqtlConfig.TMPDIR, pheno_filename), "wb")
+        output_file = open("%s%s.txt" % (TMPDIR, pheno_filename), "wb")
         header = 'FID\tIID\t%s\n' % self.this_trait.name
         output_file.write(header)
     
@@ -611,7 +580,7 @@ class MarkerRegression(object):
         
     def gen_pheno_txt_file_rqtl(self, pheno_filename = ''):
         ped_sample_list = self.get_samples_from_ped_file()	
-        output_file = open("%s%s.txt" % (webqtlConfig.TMPDIR, pheno_filename), "wb")
+        output_file = open("%s%s.txt" % (TMPDIR, pheno_filename), "wb")
         header = 'FID\tIID\t%s\n' % self.this_trait.name
         output_file.write(header)
     
@@ -756,7 +725,7 @@ class MarkerRegression(object):
     
         threshold_p_value = 0.01
     
-        result_fp = open("%s%s.qassoc"% (webqtlConfig.TMPDIR, output_filename), "rb")
+        result_fp = open("%s%s.qassoc"% (TMPDIR, output_filename), "rb")
         
         header_line = result_fp.readline()# read header line
         line = result_fp.readline()
@@ -866,9 +835,7 @@ class MarkerRegression(object):
                 Redis.expire(key, 60*60)
     
                 command = PYLMM_COMMAND+' --key {} --species {}'.format(key,"other")
-    
-                os.system(command)
-    
+                shell(command)
                 
                 json_results = Redis.blpop("pylmm:results:" + temp_uuid, 45*60)
                 results = json.loads(json_results[1])
@@ -943,12 +910,11 @@ 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")
 
-            os.system(command)
+            shell(command)
 
             #t_stats, p_values = lmm.run(key)
             #lmm.run(key)
@@ -985,8 +951,7 @@ class MarkerRegression(object):
 
     #def gen_human_results(self, pheno_vector, tempdata):
     def gen_human_results(self, pheno_vector, key, temp_uuid):
-        file_base = os.path.join(webqtlConfig.PYLMM_PATH, self.dataset.group.name)
-        print("file_base:", file_base)
+        file_base = locate(self.dataset.group.name,"mapping")
 
         plink_input = input.plink(file_base, type='b')
         input_file_name = os.path.join(webqtlConfig.SNP_PATH, self.dataset.group.name + ".snps.gz")
@@ -1078,7 +1043,11 @@ class MarkerRegression(object):
         return trimmed_genotype_data
     
 def create_snp_iterator_file(group):
-    plink_file_base = os.path.join(webqtlConfig.PYLMM_PATH, group)
+    """ 
+    This function is only called by main below
+    """
+    raise Exception("Paths are undefined here")
+    plink_file_base = os.path.join(TMPDIR, group)
     plink_input = input.plink(plink_file_base, type='b')
     
     data = dict(plink_input = list(plink_input),
@@ -1139,5 +1108,3 @@ def get_markers_from_csv(included_markers, p_values, group_name):
     
 if __name__ == '__main__':
     import cPickle as pickle
-    import gzip
-    create_snp_iterator_file("HLC")
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index e0007455..11e312b2 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -38,21 +38,11 @@ from htmlgen import HTMLgen2 as HT
 
 from base import webqtlConfig
 from base.GeneralObject import GeneralObject
-#from base.webqtlTrait import webqtlTrait
-#from base.templatePage import templatePage
 from utility import webqtlUtil
 from utility import helper_functions
 from utility import Plot
-#from utility.THCell import THCell
-#from utility.TDCell import TDCell
 from wqflask.interval_analyst import GeneUtil
 
-#from dbFunction import webqtlDatabaseFunction
-
-#import logging
-#logging.basicConfig(filename="/tmp/gn_leiyan.log", level=logging.INFO)
-#_log = logging.getLogger("gn\web\webqtl\intervalMapping\IntervalMappingPage.py")
-
 #########################################
 #      Inteval Mapping Plot Page
 #########################################
@@ -178,8 +168,8 @@ class MarkerRegression(object):
         self.species = start_vars['species']
 
         #Needing for form submission when doing single chr mapping or remapping after changing options
-        self.vals = start_vars['vals'] 
-        self.mapping_method = start_vars['mapping_method'] 
+        self.vals = start_vars['vals']
+        self.mapping_method = start_vars['mapping_method']
         if self.mapping_method == "rqtl_geno":
             self.mapmethod_rqtl_geno = start_vars['method']
             self.mapmodel_rqtl_geno = start_vars['model']
@@ -232,7 +222,7 @@ class MarkerRegression(object):
                 self.significant = start_vars['significant']
         else:
             self.nperm = 0
-           
+
         if 'bootCheck' in start_vars.keys():
             self.bootChecked = start_vars['bootCheck']
         else:
@@ -308,7 +298,7 @@ class MarkerRegression(object):
         if 'showSNP' in start_vars.keys():
             self.SNPChecked = start_vars['showSNP']
         else:
-            self.SNPChecked = False  
+            self.SNPChecked = False
         if 'showGenes' in start_vars.keys():
             self.geneChecked = start_vars['showGenes']
         else:
@@ -321,7 +311,7 @@ class MarkerRegression(object):
             self.endMb = float(start_vars['endMb'])
         except:
             self.endMb = -1
-        try: 
+        try:
             self.lrsMax = float(start_vars['lrsMax'])
         except:
             self.lrsMax = 0
@@ -363,7 +353,7 @@ class MarkerRegression(object):
             self.ChrList.append((indChr.name, i))
 
 
-        
+
         self.ChrLengthMbList = g.db.execute("""
                 Select
                         Length from Chr_Length, InbredSet
@@ -517,20 +507,19 @@ class MarkerRegression(object):
             chrName = self.selectedChr
             # Draw the genes for this chromosome / region of this chromosome
             webqtldatabase = self.dataset.name
-        
+
             if self.dataset.group.species == "mouse":
-               self.geneCol = GeneUtil.loadGenes(chrName, self.diffCol, self.startMb, self.endMb, webqtldatabase, "mouse")
+                self.geneCol = GeneUtil.loadGenes(chrName, self.diffCol, self.startMb, self.endMb, webqtldatabase, "mouse")
             elif self.dataset.group.species == "rat":
                self.geneCol = GeneUtil.loadGenes(chrName, self.diffCol, self.startMb, self.endMb, webqtldatabase, "rat")
 
-        
             if self.geneCol and self.intervalAnalystChecked:
                #######################################################################
                #Nick use GENEID as RefGene to get Literature Correlation Informations#
                #For Interval Mapping, Literature Correlation isn't useful, so skip it#
                #through set GENEID is None                                           #
                #######################################################################
-               
+
                #GENEID = fd.formdata.getvalue('GeneId') or None
                GENEID = None
 
@@ -538,7 +527,7 @@ class MarkerRegression(object):
                self.geneTable(self.geneCol, GENEID)
                #geneTable = self.geneTable(self.geneCol, GENEID)
                #geneTableContainer.append(geneTable)
-               
+
                #mainfmName = webqtlUtil.genRandStr("fm_")
                #tableForm = HT.Form(cgi=os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name=mainfmName, submit=HT.Input(type='hidden'))
                #tableForm.append(HT.Input(name='FormID', value='', type='hidden'))
@@ -553,22 +542,22 @@ class MarkerRegression(object):
         #else:
         showLocusForm = ""
         intCanvas = pid.PILCanvas(size=(self.graphWidth, self.graphHeight))
-        gifmap = self.plotIntMapping(intCanvas, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm)    
+        gifmap = self.plotIntMapping(intCanvas, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm)
 
         self.gifmap = gifmap.__str__()
         #print("GIFMAP:", gifmap.__str__())
 
         self.filename= webqtlUtil.genRandStr("Itvl_")
-        intCanvas.save(os.path.join(webqtlConfig.IMGDIR, self.filename), format='jpeg')
+        intCanvas.save(os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, self.filename), format='jpeg')
         intImg=HT.Image('/image/'+self.filename+'.png', border=0, usemap='#WebQTLImageMap')
 
         #Scales plot differently for high resolution
         if self.draw2X:
             intCanvasX2 = pid.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.IMGDIR, self.filename+"X2"), format='png')
+            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')
- 
+
         #textUrl = self.writeQTL2Text(fd, self.filename)
 
         ################################################################
@@ -598,7 +587,7 @@ class MarkerRegression(object):
             showLocusForm.append(intImg)
         else:
             showLocusForm = intImg
-        
+
         if self.permChecked and self.nperm > 0 and not self.multipleInterval and 0 < self.nperm:
             self.perm_filename = self.drawPermutationHistogram()
             #perm_text_file = self.permutationTextFile()
@@ -668,7 +657,7 @@ class MarkerRegression(object):
             TD_LR.append(HT.Blockquote(tableForm))
 
         self.body = TD_LR
-       
+
         #self.dict['body'] = TD_LR
         #self.dict['title'] = "Mapping"
 
@@ -859,7 +848,7 @@ class MarkerRegression(object):
         BootCoord = []
         i = 0
         startX = xLeftOffset
-        
+
         if self.selectedChr == -1: #ZS: If viewing full genome/all chromosomes
             for j, _chr in enumerate(self.genotype):
                 BootCoord.append( [])
@@ -882,8 +871,8 @@ class MarkerRegression(object):
                         else:
                             Xc = startX + (_locus.cM-_chr[0].cM)*plotXScale
                         BootCoord[-1].append([Xc, self.bootResult[i]])
-                    i += 1      
-                
+                    i += 1
+
         #reduce bootResult
         if self.selectedChr > -1:
             maxBootBar = 80.0
@@ -941,7 +930,7 @@ class MarkerRegression(object):
         bootScale = bootScale[:-1] + [highestPercent]
 
         bootOffset = 50*fontZoom
-        bootScaleFont=pid.Font(ttf="verdana",size=13*fontZoom,bold=0)
+        bootScaleFont=Font(ttf="verdana",size=13*fontZoom,bold=0)
         canvas.drawRect(canvas.size[0]-bootOffset,yZero-bootHeightThresh,canvas.size[0]-bootOffset-15*zoom,yZero,fillColor = pid.yellow)
         canvas.drawLine(canvas.size[0]-bootOffset+4, yZero, canvas.size[0]-bootOffset, yZero, color=pid.black)
         canvas.drawString('0%' ,canvas.size[0]-bootOffset+10,yZero+5,font=bootScaleFont,color=pid.black)
@@ -1412,7 +1401,7 @@ class MarkerRegression(object):
             if _strains[ii] in self.dataset.group.samplelist:
                 temp = GeneralObject(name=_strains[ii], value=_val)
                 smd.append(temp)
-            
+
 
         smd.sort(lambda A, B: cmp(A.value, B.value))
         smd.reverse()
@@ -1567,14 +1556,14 @@ class MarkerRegression(object):
                     firstGene = 0
                 else:
                     lastGene = 0
-                     
+
         for j, _geno in enumerate (self.genotype[0][1].genotype):
 
             plotbxd=0
             for item in smd:
                 if item.name == samplelist[j]:
-                    plotbxd=1    
-                    
+                    plotbxd=1
+
             if (plotbxd == 1):
 
                 ind = 0
@@ -1621,28 +1610,28 @@ class MarkerRegression(object):
 
         currentChromosome = self.genotype[0].name
         i = 0
-        
+
         paddingTop = yTopOffset
         ucscPaddingTop = paddingTop + self.WEBQTL_BAND_HEIGHT + self.BAND_SPACING
         ensemblPaddingTop = ucscPaddingTop + self.UCSC_BAND_HEIGHT + self.BAND_SPACING
-        
+
         if zoom == 1:
             for pixel in range(xLeftOffset, xLeftOffset + plotWidth, pixelStep):
-    
+
                 calBase = self.kONE_MILLION*(startMb + (endMb-startMb)*(pixel-xLeftOffset-0.0)/plotWidth)
-    
+
                 xBrowse1 = pixel
                 xBrowse2 = min(xLeftOffset + plotWidth, (pixel + pixelStep - 1))
-    
+
                 WEBQTL_COORDS = "%d, %d, %d, %d" % (xBrowse1, paddingTop, xBrowse2, (paddingTop+self.WEBQTL_BAND_HEIGHT))
                 bandWidth = xBrowse2 - xBrowse1
                 WEBQTL_HREF = "javascript:rangeView('%s', %f, %f)" % (self.selectedChr - 1, max(0, (calBase-webqtlZoomWidth))/1000000.0, (calBase+webqtlZoomWidth)/1000000.0)
-    
+
                 WEBQTL_TITLE = "Click to view this section of the genome in WebQTL"
                 gifmap.areas.append(HT.Area(shape='rect',coords=WEBQTL_COORDS,href=WEBQTL_HREF, title=WEBQTL_TITLE))
                 canvas.drawRect(xBrowse1, paddingTop, xBrowse2, (paddingTop + self.WEBQTL_BAND_HEIGHT), edgeColor=self.CLICKABLE_WEBQTL_REGION_COLOR, fillColor=self.CLICKABLE_WEBQTL_REGION_COLOR)
                 canvas.drawLine(xBrowse1, paddingTop, xBrowse1, (paddingTop + self.WEBQTL_BAND_HEIGHT), color=self.CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR)
-    
+
                 UCSC_COORDS = "%d, %d, %d, %d" %(xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop+self.UCSC_BAND_HEIGHT))
                 if self.dataset.group.species == "mouse":
                     UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d&hgt.customText=%s/snp/chr%s" % (self._ucscDb, self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases, webqtlConfig.PORTADDR, self.selectedChr)
@@ -1652,7 +1641,7 @@ class MarkerRegression(object):
                 gifmap.areas.append(HT.Area(shape='rect',coords=UCSC_COORDS,href=UCSC_HREF, title=UCSC_TITLE))
                 canvas.drawRect(xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop+self.UCSC_BAND_HEIGHT), edgeColor=self.CLICKABLE_UCSC_REGION_COLOR, fillColor=self.CLICKABLE_UCSC_REGION_COLOR)
                 canvas.drawLine(xBrowse1, ucscPaddingTop, xBrowse1, (ucscPaddingTop+self.UCSC_BAND_HEIGHT), color=self.CLICKABLE_UCSC_REGION_OUTLINE_COLOR)
-    
+
                 ENSEMBL_COORDS = "%d, %d, %d, %d" %(xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop+self.ENSEMBL_BAND_HEIGHT))
                 if self.dataset.group.species == "mouse":
                     ENSEMBL_HREF = "http://www.ensembl.org/Mus_musculus/contigview?highlight=&chr=%s&vc_start=%d&vc_end=%d&x=35&y=12" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
@@ -1767,7 +1756,7 @@ class MarkerRegression(object):
             ChrAInfo = []
             preLpos = -1
             distinctCount = 0.0
-            
+
             #if len(self.genotype) > 1:
             if self.selectedChr == -1: #ZS: If viewing full genome/all chromosomes
                 for i, _chr in enumerate(self.genotype):
@@ -1810,7 +1799,7 @@ class MarkerRegression(object):
             offsetA = -stepA
             lineColor = pid.lightblue
             startPosX = xLeftOffset
-            
+
             for j, ChrInfo in enumerate(ChrAInfo):
                 preLpos = -1
                 for i, item in enumerate(ChrInfo):
@@ -1878,7 +1867,7 @@ class MarkerRegression(object):
             # lodm = self.LODFACTOR
         # else:
             # lodm = 1.0
- 
+
         #ZS: This is a mess, but I don't know a better way to account for different mapping methods returning results in different formats + the option to change between LRS and LOD
         if self.lrsMax <= 0:  #sliding scale
             if "lrs_value" in self.qtlresults[0]:
@@ -1891,7 +1880,7 @@ class MarkerRegression(object):
                 else:
                     if self.permChecked and self.nperm > 0 and not self.multipleInterval:
                         self.significant = min(self.significant, webqtlConfig.MAXLRS)
-                        self.suggestive = min(self.suggestive, webqtlConfig.MAXLRS)                    
+                        self.suggestive = min(self.suggestive, webqtlConfig.MAXLRS)
                     else:
                         pass
             else:
@@ -1904,10 +1893,10 @@ class MarkerRegression(object):
                 else:
                     if self.permChecked and self.nperm > 0 and not self.multipleInterval:
                         self.significant = min(self.significant, webqtlConfig.MAXLRS)
-                        self.suggestive = min(self.suggestive, webqtlConfig.MAXLRS)  
+                        self.suggestive = min(self.suggestive, webqtlConfig.MAXLRS)
                     else:
                         pass
-                        
+
             if self.permChecked and self.nperm > 0 and not self.multipleInterval:
                 LRS_LOD_Max = max(self.significant, LRS_LOD_Max)
 
@@ -1924,7 +1913,7 @@ class MarkerRegression(object):
             LRSScale = 2.5
         else:
             LRSScale = 1.0
-           
+
         LRSAxisList = Plot.frange(LRSScale, LRS_LOD_Max, LRSScale)
         #make sure the user's value appears on the y-axis
         #update by NL 6-21-2011: round the LOD value to 100 when LRS_LOD_Max is equal to 460
@@ -1954,7 +1943,7 @@ class MarkerRegression(object):
 
             #"Significant" and "Suggestive" Drawing Routine
             # ======= Draw the thick lines for "Significant" and "Suggestive" =====  (crowell: I tried to make the SNPs draw over these lines, but piddle wouldn't have it...)
-            
+
             #ZS: I don't know if what I did here with this inner function is clever or overly complicated, but it's the only way I could think of to avoid duplicating the code inside this function
             def add_suggestive_significant_lines_and_legend(start_pos_x, chr_length_dist):
                 rightEdge = int(start_pos_x + chr_length_dist*plotXScale - self.SUGGESTIVE_WIDTH/1.5)
@@ -1977,13 +1966,13 @@ class MarkerRegression(object):
 
                 start_pos_x +=  (chr_length_dist+self.GraphInterval)*plotXScale
                 return start_pos_x
-            
+
             for i, _chr in enumerate(self.genotype):
                 if self.selectedChr != -1:
                     if _chr.name == self.ChrList[self.selectedChr][0]:
                         startPosX = add_suggestive_significant_lines_and_legend(startPosX, self.ChrLengthDistList[0])
                         break
-                    else: 
+                    else:
                         continue
                 else:
                     startPosX = add_suggestive_significant_lines_and_legend(startPosX, self.ChrLengthDistList[i])
@@ -1998,7 +1987,7 @@ class MarkerRegression(object):
             #else:
             #    dominanceMax = -1
             lrsEdgeWidth = 2
-            
+
         if zoom == 2:
             lrsEdgeWidth = 2 * lrsEdgeWidth
 
@@ -2019,7 +2008,7 @@ class MarkerRegression(object):
             if qtlresult['chr'] != previous_chr and self.selectedChr == -1:
                 if self.manhattan_plot != True:
                     canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
-                    
+
                 if not self.multipleInterval and self.additiveChecked:
                     plusColor = self.ADDITIVE_COLOR_POSITIVE
                     minusColor = self.ADDITIVE_COLOR_NEGATIVE
@@ -2049,7 +2038,7 @@ class MarkerRegression(object):
                                     canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
                                 else:
                                     canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
-                    
+
                 LRSCoordXY = []
                 AdditiveCoordXY = []
                 previous_chr = qtlresult['chr']
@@ -2062,7 +2051,7 @@ class MarkerRegression(object):
 
             #startPosX += (self.ChrLengthDistList[j]+self.GraphInterval)*plotXScale
 
-            #for j, _chr in enumerate(self.genotype):   
+            #for j, _chr in enumerate(self.genotype):
             #ZS: This is beause the chromosome value stored in qtlresult['chr'] can be (for example) either X or 20 depending upon the mapping method/scale used
             if self.plotScale == "physic":
                 this_chr = str(self.ChrList[self.selectedChr][0])
@@ -2126,7 +2115,7 @@ class MarkerRegression(object):
 
         if self.manhattan_plot != True:
             canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
-            
+
         if not self.multipleInterval and self.additiveChecked:
             plusColor = self.ADDITIVE_COLOR_POSITIVE
             minusColor = self.ADDITIVE_COLOR_NEGATIVE
@@ -2156,7 +2145,7 @@ class MarkerRegression(object):
                             canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
                         else:
                             canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
-                    
+
         if not self.multipleInterval and INTERCROSS and self.dominanceChecked:
             plusColor = self.DOMINANCE_COLOR_POSITIVE
             minusColor = self.DOMINANCE_COLOR_NEGATIVE
@@ -2186,7 +2175,7 @@ class MarkerRegression(object):
                             canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
                         else:
                             canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
-                
+
 
         ###draw additive scale
         if not self.multipleInterval and self.additiveChecked:
@@ -2222,7 +2211,7 @@ class MarkerRegression(object):
         if zoom == 2:
             fontZoom = 1.5
             yTopOffset += 30
-        
+
         #calculate plot scale
         if self.plotScale != 'physic':
             self.ChrLengthDistList = self.ChrLengthCMList
@@ -2589,13 +2578,13 @@ class MarkerRegression(object):
             perm_output = [value/4.16 for value in self.perm_output]
         else:
             perm_output = self.perm_output
-            
+
         Plot.plotBar(myCanvas, perm_output, XLabel=self.LRS_LOD, YLabel='Frequency', title=' Histogram of Permutation Test')
         filename= webqtlUtil.genRandStr("Reg_")
         myCanvas.save(webqtlConfig.IMGDIR+filename, format='gif')
-        
+
         return filename
-        
+
         # img=HT.Image('/image/'+filename+'.gif',border=0,alt='Histogram of Permutation Test')
 
         # self.suggestive = self.perm_output[int(self.nperm*0.37-1)]
@@ -2609,9 +2598,9 @@ class MarkerRegression(object):
         # permutation.append(HT.TR(HT.TD(img)),
                            # HT.TR(HT.TD('')),
                            # HT.TR(HT.TD('Total of %d permutations'%self.nperm)))
-        
+
         # return permutation
-    
+
     def permutationTextFile(self):
         filename= webqtlUtil.genRandStr("Reg_")
         fpText = open('%s.txt' % (webqtlConfig.TMPDIR+filename), 'wb')
@@ -2624,12 +2613,12 @@ class MarkerRegression(object):
                               '&nbsp;&nbsp;&nbsp;&nbsp;Significant LRS =%3.2f\n'%self.significant,
                               HT.BR(),
                               '&nbsp;&nbsp;&nbsp;&nbsp;Highly Significant LRS =%3.2f\n' % self.highlysignificant)
-        
+
         for lrs_value in self.perm_output:
             fpText.write(str(lrs_value) + "\n")
-        
+
         textUrl = HT.Href(text = 'Download Permutation Results', url= '/tmp/'+filename+'.txt', target = "_blank", Class='fs12 fwn')
-        
+
         return textUrl
 
     def geneTable(self, geneCol, refGene=None):
@@ -3039,4 +3028,4 @@ class MarkerRegression(object):
 
         sortby = ("", "")
 
-        return sortby
\ No newline at end of file
+        return sortby
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index a57bfffe..9941a4d3 100755
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -24,9 +24,8 @@ from flask import Flask, g
 from MySQLdb import escape_string as escape
 
 # Instead of importing HT we're going to build a class below until we can eliminate it
-from htmlgen import HTMLgen2 as HT
+# from htmlgen import HTMLgen2 as HT
 
-from base import webqtlConfig
 from utility.benchmark import Bench
 from base.data_set import create_dataset
 from base.trait import GeneralTrait
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 2d4c952a..79f1c867 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -16,7 +16,6 @@ from base import webqtlConfig
 from base import webqtlCaseData
 from wqflask.show_trait.SampleList import SampleList
 from utility import webqtlUtil, Plot, Bunch, helper_functions
-from utility.tools import pylmm_command, plink_command
 from base.trait import GeneralTrait
 from base import data_set
 from dbFunction import webqtlDatabaseFunction
@@ -24,8 +23,8 @@ from basicStatistics import BasicStatisticsFunctions
 
 from pprint import pformat as pf
 
-PYLMM_PATH,PYLMM_COMMAND = pylmm_command()
-PLINK_PATH,PLINK_COMMAND = plink_command()
+from utility.tools import flat_files
+MAPPING_PATH = flat_files("mapping")
 
 ###############################################
 #
@@ -34,8 +33,6 @@ PLINK_PATH,PLINK_COMMAND = plink_command()
 #
 ##############################################
 
-
-
 class ShowTrait(object):
 
     def __init__(self, kw):
@@ -162,14 +159,14 @@ class ShowTrait(object):
     def get_mapping_methods(self):
         '''Only display mapping methods when the dataset group's genotype file exists'''
         def check_plink_gemma():
-            if (os.path.isfile(PLINK_PATH+"/"+self.dataset.group.name+".bed") and
-                os.path.isfile(PLINK_PATH+"/"+self.dataset.group.name+".map")):
+            if (os.path.isfile(MAPPING_PATH+"/"+self.dataset.group.name+".bed") and
+                os.path.isfile(MAPPING_PATH+"/"+self.dataset.group.name+".map")):
                 return True
             else:
                 return False
 
         def check_pylmm_rqtl():
-            if os.path.isfile(webqtlConfig.GENODIR+self.dataset.group.name+".geno") and (os.path.getsize(webqtlConfig.NEWGENODIR+self.dataset.group.name+".json") > 0):
+            if os.path.isfile(webqtlConfig.GENODIR+self.dataset.group.name+".geno") and (os.path.getsize(webqtlConfig.JSON_GENODIR+self.dataset.group.name+".json") > 0):
                 return True
             else:
                 return False
diff --git a/wqflask/wqflask/static/css b/wqflask/wqflask/static/css
deleted file mode 120000
index 9d8c2f68..00000000
--- a/wqflask/wqflask/static/css
+++ /dev/null
@@ -1 +0,0 @@
-../../../web/css
\ No newline at end of file
diff --git a/wqflask/wqflask/static/dbdoc/TODO.md b/wqflask/wqflask/static/dbdoc/TODO.md
deleted file mode 100644
index c0a8bab7..00000000
--- a/wqflask/wqflask/static/dbdoc/TODO.md
+++ /dev/null
@@ -1 +0,0 @@
-TODO: Add all database documentation into this folder
diff --git a/wqflask/wqflask/static/images b/wqflask/wqflask/static/images
deleted file mode 120000
index 12f0f8b5..00000000
--- a/wqflask/wqflask/static/images
+++ /dev/null
@@ -1 +0,0 @@
-../../../web/images
\ No newline at end of file
diff --git a/wqflask/wqflask/static/javascript b/wqflask/wqflask/static/javascript
deleted file mode 120000
index 5f58faf4..00000000
--- a/wqflask/wqflask/static/javascript
+++ /dev/null
@@ -1 +0,0 @@
-../../../web/javascript
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/css/corr_matrix.css b/wqflask/wqflask/static/new/css/corr_matrix.css
index 495ca28c..cd2b0a80 100755
--- a/wqflask/wqflask/static/new/css/corr_matrix.css
+++ b/wqflask/wqflask/static/new/css/corr_matrix.css
@@ -3,7 +3,7 @@
        -moz-transform: rotate(-90deg);
         -ms-transform: rotate(-90deg);
          -o-transform: rotate(-90deg);
-            trasnform: rotate(-90deg);
+            transform: rotate(-90deg);
               color: #000
               font-size: 22px;
               height: 50px;
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index f92d9984..c1563b9c 100755
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -55,6 +55,18 @@
                     <input type="submit" class="btn btn-primary" value="WGCNA Analysis" />
                 </div>
             </form>
+            <form action="/ctl_setup" method="post">
+                {% if uc %}
+                <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" />
+                {% endif %}
+                <input type="hidden" name="trait_list" id="trait_list" value= "
+                {% for this_trait in trait_obs %}
+                    {{ this_trait.name }}:{{ this_trait.dataset.name }},
+                {% endfor %}" >
+                <div class="col-xs-2 controls">
+                    <input type="submit" class="btn btn-primary" value="CTL Analysis" />
+                </div>
+            </form>
             <form action="/heatmap" method="post">
                 {% if uc %}
                 <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" />
diff --git a/wqflask/wqflask/templates/ctl_results.html b/wqflask/wqflask/templates/ctl_results.html
new file mode 100644
index 00000000..a5cb1c08
--- /dev/null
+++ b/wqflask/wqflask/templates/ctl_results.html
@@ -0,0 +1,47 @@
+{% extends "base.html" %}
+{% block title %}CTL results{% endblock %}
+
+{% block content %} <!-- Start of body -->
+<div class="container">
+  <h1>CTL Results</h1>
+  {{(request.form['trait_list'].split(',')|length -1)}} phenotypes as input<br>
+  <h3>Network Figure</h3>
+  <a href="/tmp/{{ results['imgurl1'] }}">
+      <img alt="Embedded Image" src="data:image/png;base64,
+      {% for elem in results['imgdata1'] -%}
+      {% print("%c"|format(elem)) %}
+      {%- endfor %}
+      " /></a>
+  <h3>CTL/QTL Plots for individual traits</h3>
+  {% for r in range(2, (request.form['trait_list'].split(',')|length +1)) %}
+  <a href="/tmp/{{ results['imgurl' + r|string] }}">
+      <img width=100 height=100 alt="Embedded Image" src="data:image/png;base64,
+      {% for elem in results['imgdata' + r|string] -%}
+      {% print("%c"|format(elem)) %}
+      {%- endfor %}
+      " /></a>
+  {% endfor %}
+  <h3>Tabular results</h3>
+  <table width="80%">
+  <tr><th>trait</th><th>marker</th><th>trait</th><th>LOD</th><th>dCor</th></tr>
+  significant CTL:<br>
+  {% for r in range(results['ctlresult'][0]|length) %}
+    <tr>
+    {% for c in range(results['ctlresult']|length) %}
+      <td>
+      {% if c > 2 %}
+      {{results['ctlresult'][c][r]|float|round(2)}}
+      {% else %}
+      {{results['ctlresult'][c][r]}}
+      {% endif %}
+      </td>
+    {% endfor %}
+    </tr>
+  {% endfor %}
+  </table>
+
+
+
+
+</div>
+{% endblock %}
diff --git a/wqflask/wqflask/templates/ctl_setup.html b/wqflask/wqflask/templates/ctl_setup.html
new file mode 100644
index 00000000..9c0d7bea
--- /dev/null
+++ b/wqflask/wqflask/templates/ctl_setup.html
@@ -0,0 +1,65 @@
+{% extends "base.html" %}
+{% block title %}WCGNA analysis{% endblock %}
+
+{% block content %} <!-- Start of body -->
+<div class="container">
+  <h1>CTL analysis parameters</h1>
+  {{(request.form['trait_list'].split(',')|length -1)}} phenotypes as input
+
+<form action="/ctl_results" method="post" class="form-horizontal">
+	<input type="hidden" name="trait_list" id="trait_list" value= "{{request.form['trait_list']}}">
+
+	<div class="dropdown">
+		<label for="Strategy">Strategy</label>
+		<div class="col-sm-10">
+		<select  name="strategy" id="strategy">
+			<option value="Exact">Exact</option>
+			<option value="Full">Full</option>
+			<option value="Pairwise">Pairwise</option>
+		</select>
+		</div>
+	</div>
+
+	<div class="dropdown">
+		<label for="Permutations">Number of permutation (Used when strategy is Full or Pairwise)</label>
+		<div class="col-sm-10">
+		<select  name="nperm" id="nperm">
+			<option value="100">100</option>
+			<option value="1000" selected="selected">1000</option>
+			<option value="10000">10000</option>
+		</select>
+		</div>
+	</div>
+
+	<div class="dropdown">
+		<label for="Coefficient">Type of correlation coefficient</label>
+		<div class="col-sm-10">
+		<select  name="parametric" id="parametric">
+			<option value="False">Spearman</option>
+			<option value="True">Pearson</option>
+		</select>
+		</div>
+	</div>
+
+
+	<div class="dropdown">
+		<label for="Significance">Significance level</label>
+		<div class="col-sm-10">
+		<select  name="significance" id="significance">
+			<option value="0.1">0.1</option>
+			<option value="0.05" selected="selected">0.05</option>
+			<option value="0.001">0.001</option>
+		</select>
+		</div>
+	</div>
+  <br>
+	<div class="form-group">
+		<div class="col-sm-10">
+			<input type="submit" class="btn btn-primary" value="Run CTL using these settings" />
+		</div>
+	</div>
+
+</form>
+
+</div>
+{% endblock %}
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index 7f269048..07f764ca 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -143,7 +143,7 @@
             <div class="tab-pane active" id="gn1_map">
               <div class="qtlcharts">
                   {{ gifmap|safe }}
-                  <img src="/static/output/{{ filename }}.jpeg" usemap="#WebQTLImageMap">
+                  <img src="/generated/{{ filename }}.jpeg" usemap="#WebQTLImageMap">
                   {% if additiveChecked|upper == "ON" %}
                   <br>
                   <span style="white-space: nowrap;">A positive additive coefficient (green line) indicates that {{ dataset.group.parlist[1] }} alleles increase trait values. In contrast, a negative additive coefficient (orange line) indicates that {{ dataset.group.parlist[0] }} alleles increase trait values.</span>
diff --git a/wqflask/wqflask/templates/wgcna_setup.html b/wqflask/wqflask/templates/wgcna_setup.html
index 8ab8c4a0..b4a5730d 100644
--- a/wqflask/wqflask/templates/wgcna_setup.html
+++ b/wqflask/wqflask/templates/wgcna_setup.html
@@ -17,36 +17,36 @@
     {% else %}
  		<form action="/wgcna_results" method="post" class="form-horizontal">
 				<input type="hidden" name="trait_list" id="trait_list" value= "{{request.form['trait_list']}}">
-				<div class="form-group">			
+				<div class="form-group">
 					<label for="SoftThresholds"> Soft threshold: </label>
 					<div class="col-sm-10">
 						<input type="text" class="form-inline" name="SoftThresholds" id="SoftThresholds" value="1,2,3,4,5,6,7,8,9">
 					</div>
 				</div>
-				<div class="form-group">			
+				<div class="form-group">
 					<label for="MinModuleSize"> Minimum module size: </label>
 					<div class="col-sm-10">
 						<input type="text" class="form-inline" name="MinModuleSize" id="MinModuleSize" value="30">
 					</div>
 				</div>
-				<div class="form-group">			
+				<div class="form-group">
 					<label for="TOMtype"> TOMtype: </label>
 					<div class="col-sm-10">
 						<input type="text" class="form-inline" name="TOMtype" id="TOMtype" value="unsigned">
 					</div>
-				</div>			
-				<div class="form-group">			
+				</div>
+				<div class="form-group">
 					<label for="mergeCutHeight"> mergeCutHeight: </label>
 					<div class="col-sm-10">
 						<input type="text" class="form-inline" name="mergeCutHeight" id="mergeCutHeight" value="0.25">
 					</div>
-				</div>			
-				<div class="form-group">			
+				</div>
+				<div class="form-group">
 					<div class="col-sm-10">
 						<input type="submit" class="btn btn-primary" value="Run WGCNA using these settings" />
 					</div>
-				</div>			
-		</form>		
+				</div>
+		</form>
 		{% endif %}
 </div>
 {% endblock %}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 3bf64a18..87ba8b32 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -30,7 +30,7 @@ import sqlalchemy
 from wqflask import app
 
 from flask import (render_template, request, make_response, Response,
-                   Flask, g, config, jsonify, redirect, url_for)
+                   Flask, g, config, jsonify, redirect, url_for, send_from_directory)
 
 from wqflask import search_results
 from wqflask import gsearch
@@ -48,10 +48,13 @@ from wqflask.correlation_matrix import show_corr_matrix
 from wqflask.correlation import corr_scatter_plot
 
 from wqflask.wgcna import wgcna_analysis
+from wqflask.ctl import ctl_analysis
 
 from utility import temp_data
+from utility.tools import TEMPDIR
 
 from base import webqtlFormData
+from base.webqtlConfig import GENERATED_IMAGE_DIR
 from utility.benchmark import Bench
 
 from pprint import pformat as pf
@@ -96,7 +99,7 @@ def tmp_page(img_path):
     print("img_path:", img_path)
     initial_start_vars = request.form
     print("initial_start_vars:", initial_start_vars)
-    imgfile = open(webqtlConfig.TMPDIR + img_path, 'rb')
+    imgfile = open(GENERATED_IMAGE_DIR + img_path, 'rb')
     imgdata = imgfile.read()
     imgB64 = imgdata.encode("base64")
     bytesarray = array.array('B', imgB64)
@@ -172,6 +175,10 @@ def docedit():
     doc = docs.Docs(request.args['entry'])
     return render_template("docedit.html", **doc.__dict__)
 
+@app.route('/generated/<filename>')
+def generated_file(filename):
+    return send_from_directory(GENERATED_IMAGE_DIR,filename)
+
 @app.route("/help")
 def help():
     doc = docs.Docs("help")
@@ -190,6 +197,18 @@ def wcgna_results():
     result = wgcna.process_results(wgcnaA)                        # After the analysis is finished store the result
     return render_template("wgcna_results.html", **result)        # Display them using the template
 
+@app.route("/ctl_setup", methods=('POST',))
+def ctl_setup():
+    print("In ctl, request.form is:", request.form)             # We are going to get additional user input for the analysis
+    return render_template("ctl_setup.html", **request.form)          # Display them using the template
+
+@app.route("/ctl_results", methods=('POST',))
+def ctl_results():
+    print("In ctl, request.form is:", request.form)
+    ctl = ctl_analysis.CTL()                                  # Start R, load the package and pointers and create the analysis
+    ctlA = ctl.run_analysis(request.form)                     # Start the analysis, a ctlA object should be a separate long running thread
+    result = ctl.process_results(ctlA)                        # After the analysis is finished store the result
+    return render_template("ctl_results.html", **result)      # Display them using the template
 
 @app.route("/news")
 def news_route():
@@ -423,7 +442,7 @@ def marker_regression_page():
             print("img_path:", img_path)
             initial_start_vars = request.form
             print("initial_start_vars:", initial_start_vars)
-            imgfile = open('/home/zas1024/tmp/' + img_path, 'rb')
+            imgfile = open(TEMPDIR + '/' + img_path, 'rb')
             imgdata = imgfile.read()
             imgB64 = imgdata.encode("base64")
             bytesarray = array.array('B', imgB64)
@@ -452,7 +471,7 @@ def export_pdf():
     svg_xml = request.form.get("data", "Invalid data")
     print("svg_xml:", svg_xml)
     filename = request.form.get("filename", "interval_map_pdf")
-    filepath = "/home/zas1024/gene/wqflask/output/"+filename
+    filepath = GENERATED_IMAGE_DIR+filename
     pdf_file = cairosvg.svg2pdf(bytestring=svg_xml)
     response = Response(pdf_file, mimetype="application/pdf")
     response.headers["Content-Disposition"] = "attachment; filename=%s"%filename
diff --git a/wqflask/wqflask/wgcna/wgcna_analysis.py b/wqflask/wqflask/wgcna/wgcna_analysis.py
index 9e9f41bc..6901712b 100644
--- a/wqflask/wqflask/wgcna/wgcna_analysis.py
+++ b/wqflask/wqflask/wgcna/wgcna_analysis.py
@@ -6,7 +6,7 @@ import scipy as sp                            # SciPy
 import rpy2.robjects as ro                    # R Objects
 import rpy2.rinterface as ri
 
-from base import webqtlConfig                 # For paths and stuff
+from base.webqtlConfig import GENERATED_IMAGE_DIR
 from utility import webqtlUtil                # Random number for the image
 
 import base64
@@ -127,7 +127,7 @@ class WGCNA(object):
 
         # The iconic WCGNA plot of the modules in the hanging tree
         self.results['imgurl'] = webqtlUtil.genRandStr("WGCNAoutput_") + ".png"
-        self.results['imgloc'] = webqtlConfig.TMPDIR + self.results['imgurl']
+        self.results['imgloc'] = GENERATED_IMAGE_DIR + self.results['imgurl']
         r_png(self.results['imgloc'], width=1000, height=600)
         mergedColors = self.r_labels2colors(network[1])
         self.r_plotDendroAndColors(network[5][0], mergedColors, "Module colors", dendroLabels = False, hang = 0.03, addGuide = True, guideHang = 0.05)