From 7f5536635ac20f7c670e4dc8e650f27d47503d78 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 15 Feb 2016 18:00:18 +0000
Subject: Fixed R/qtl mapping so the group (BXD, etc) isn't hardcoded
Removed an extraneous </td> tag from the show trait page
---
wqflask/other_config/nginx_conf/gn2-zach.conf | 52 ++++++++++++++++++++++
wqflask/other_config/nginx_conf/gn2_zach.conf | 52 ----------------------
.../wqflask/marker_regression/marker_regression.py | 7 ++-
wqflask/wqflask/templates/show_trait.html | 4 --
.../wqflask/templates/show_trait_statistics.html | 2 +-
5 files changed, 58 insertions(+), 59 deletions(-)
create mode 100755 wqflask/other_config/nginx_conf/gn2-zach.conf
delete mode 100755 wqflask/other_config/nginx_conf/gn2_zach.conf
diff --git a/wqflask/other_config/nginx_conf/gn2-zach.conf b/wqflask/other_config/nginx_conf/gn2-zach.conf
new file mode 100755
index 00000000..38347292
--- /dev/null
+++ b/wqflask/other_config/nginx_conf/gn2-zach.conf
@@ -0,0 +1,52 @@
+server {
+ # Modeled after http://flask.pocoo.org/docs/deploying/wsgi-standalone/
+ listen 80;
+
+ server_name gn2-zach.genenetwork.org;
+
+ access_log /var/log/nginx/access.log;
+ error_log /var/log/nginx/error.log;
+
+ location ^~ /css/ {
+ root /gene/wqflask/wqflask/static/;
+ }
+
+ location ^~ /javascript/ {
+ root /gene/wqflask/wqflask/static/;
+ }
+
+# location ^~ /image/ {
+# root /gene/wqflask/wqflask/static/;
+# }
+
+ location ^~ /images/ {
+ root /gene/wqflask/wqflask/static/;
+ }
+
+ ### New - added by Sam
+ #location ^~ /static/ {
+ # root /gene/wqflask/wqflask/static/;
+ #}
+
+ location /plink_gemma/ {
+ root /home/zas1024/gene/wqflask/wqflask/;
+ autoindex on;
+ }
+
+ location /download/ {
+ root /home/zas1024/gene/wqflask/wqflask/;
+ autoindex on;
+ }
+
+ location / {
+ proxy_pass http://127.0.0.1:5002/;
+ proxy_redirect off;
+
+ proxy_set_header Host $host;
+ proxy_set_header X-Real-IP $remote_addr;
+ proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+
+ proxy_read_timeout 40m;
+ }
+}
+
diff --git a/wqflask/other_config/nginx_conf/gn2_zach.conf b/wqflask/other_config/nginx_conf/gn2_zach.conf
deleted file mode 100755
index 1614bcb4..00000000
--- a/wqflask/other_config/nginx_conf/gn2_zach.conf
+++ /dev/null
@@ -1,52 +0,0 @@
-server {
- # Modeled after http://flask.pocoo.org/docs/deploying/wsgi-standalone/
- listen 80;
-
- server_name gn2_zach.genenetwork.org;
-
- access_log /var/log/nginx/access.log;
- error_log /var/log/nginx/error.log;
-
- location ^~ /css/ {
- root /gene/wqflask/wqflask/static/;
- }
-
- location ^~ /javascript/ {
- root /gene/wqflask/wqflask/static/;
- }
-
-# location ^~ /image/ {
-# root /gene/wqflask/wqflask/static/;
-# }
-
- location ^~ /images/ {
- root /gene/wqflask/wqflask/static/;
- }
-
- ### New - added by Sam
- #location ^~ /static/ {
- # root /gene/wqflask/wqflask/static/;
- #}
-
- location /plink_gemma/ {
- root /home/zas1024/gene/wqflask/wqflask/;
- autoindex on;
- }
-
- location /download/ {
- root /home/zas1024/gene/wqflask/wqflask/;
- autoindex on;
- }
-
- location / {
- proxy_pass http://127.0.0.1:5002/;
- proxy_redirect off;
-
- proxy_set_header Host $host;
- proxy_set_header X-Real-IP $remote_addr;
- proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
-
- proxy_read_timeout 40m;
- }
-}
-
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index d3ee344d..c16c885e 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -298,6 +298,9 @@ class MarkerRegression(object):
def geno_to_rqtl_function(self): # TODO: Need to figure out why some genofiles have the wrong format and don't convert properly
print("Adding some custom helper functions to the R environment")
+
+
+
ro.r("""
trim <- function( x ) { gsub("(^[[:space:]]+|[[:space:]]+$)", "", 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>
--
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