Fixed R/qtl mapping so the group (BXD, etc) isn't hardcoded

Removed an extraneous </td> tag from the show trait page

4 files changed, 7 insertions, 8 deletions

diff --git a/wqflask/other_config/nginx_conf/gn2_zach.conf b/wqflask/other_config/nginx_conf/gn2-zach.conf
index 1614bcb4..38347292 100755
--- a/wqflask/other_config/nginx_conf/gn2_zach.conf
+++ b/wqflask/other_config/nginx_conf/gn2-zach.conf
@@ -2,7 +2,7 @@ server {
     # Modeled after http://flask.pocoo.org/docs/deploying/wsgi-standalone/
     listen 80;
 
-    server_name gn2_zach.genenetwork.org;
+    server_name gn2-zach.genenetwork.org;
 
     access_log  /var/log/nginx/access.log;
     error_log  /var/log/nginx/error.log;
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index d3ee344d..c16c885e 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -298,6 +298,9 @@ class MarkerRegression(object):
 
     def geno_to_rqtl_function(self):        # TODO: Need to figure out why some genofiles have the wrong format and don't convert properly
         print("Adding some custom helper functions to the R environment")
+
+
+
         ro.r("""
            trim <- function( x ) { gsub("(^[[:space:]]+|[[:space:]]+$)", "", x) }
 
@@ -306,7 +309,7 @@ class MarkerRegression(object):
              return(trim(strsplit(header[mat],':')[[1]][2]))
            }
 
-           GENOtoCSVR <- function(genotypes = 'BXD.geno', out = 'cross.csvr', phenotype = NULL, sex = NULL, verbose = FALSE){
+           GENOtoCSVR <- function(genotypes = '%s', out = 'cross.csvr', phenotype = NULL, sex = NULL, verbose = FALSE){
              header = readLines(genotypes, 40)                                                                                 # Assume a geno header is not longer than 40 lines
              toskip = which(unlist(lapply(header, function(x){ length(grep("Chr\t", x)) })) == 1)-1                            # Major hack to skip the geno headers
              
@@ -325,7 +328,7 @@ class MarkerRegression(object):
              if(type == 'riset') cross <- convert2riself(cross)                                                                # If its a RIL, convert to a RIL in R/qtl
              return(cross)
           }
-        """)
+        """ % (self.dataset.group.name + ".geno"))
     
     def run_rqtl_geno(self):
         print("Calling R/qtl")
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index b4f5b6c2..29239adb 100755
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -189,8 +189,6 @@
                    }
                 });
 
-                console.time("Creating table");
-
                 $('#samples_primary, #samples_other').find("tr.outlier").css('background-color', 'yellow')
                 {% if sample_groups[0].se_exists() %} 
                 $('#samples_primary, #samples_other').DataTable( {
@@ -218,10 +216,8 @@
                     },
                     "paging": false
                 } );
-                console.timeEnd("Creating table");
 
                 {% else %}
-                console.time("Creating table");
                     
                 $('#samples_primary, #samples_other').DataTable( {
                     "columns": [
diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html
index 34fa2216..2183dd30 100755
--- a/wqflask/wqflask/templates/show_trait_statistics.html
+++ b/wqflask/wqflask/templates/show_trait_statistics.html
@@ -110,7 +110,7 @@
 
                         <div>
                             More about <a href="http://en.wikipedia.org/wiki/Normal_probability_plot" target="_blank">Normal Probability Plots</a> and more
-                            about interpreting these plots from the <a href="/glossary.html#normal_probability" target="_blank">glossary</a></td>
+                            about interpreting these plots from the <a href="/glossary.html#normal_probability" target="_blank">glossary</a>
                             </div>
 
                     </div>