diff options
Diffstat (limited to 'wqflask')
| -rwxr-xr-x | wqflask/other_config/nginx_conf/gn2-zach.conf (renamed from wqflask/other_config/nginx_conf/gn2_zach.conf) | 2 | ||||
| -rwxr-xr-x | wqflask/wqflask/marker_regression/marker_regression.py | 7 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/show_trait.html | 4 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/show_trait_statistics.html | 2 |
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> |