From 837ce8b9c779b1da6e4390220ccd353b289c1fca Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Wed, 20 Dec 2017 09:11:31 -0600
Subject: Bring in some earlier work - mostly documentation and startup
 handling

---
 wqflask/base/data_set.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask/base')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 6649f8af..a4eaaa2e 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -332,7 +332,7 @@ class DatasetGroup(object):
         if check_plink_gemma():
             marker_class = HumanMarkers
         else:
-            marker_class = Markers            
+            marker_class = Markers
 
         if self.genofile:
             self.markers = marker_class(self.genofile[:-5])
-- 
cgit v1.2.3


From 97ccc478543a7bb08fe0cf178e320dd5811d8bfa Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sat, 10 Feb 2018 07:53:53 +0000
Subject: Check for bimbam path and bail out if it is missing

---
 bin/genenetwork2             | 1 +
 wqflask/base/webqtlConfig.py | 1 +
 wqflask/utility/tools.py     | 4 ----
 3 files changed, 2 insertions(+), 4 deletions(-)

(limited to 'wqflask/base')

diff --git a/bin/genenetwork2 b/bin/genenetwork2
index f64576d5..7148c022 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -45,6 +45,7 @@
 
 SCRIPT=$(realpath "$0")
 echo SCRIPT=$SCRIPT
+echo GN2_PROFILE=$GN2_PROFILE
 GN2_BASE_DIR=$(dirname $(dirname "$SCRIPT"))
 GN2_ID=$(cat /etc/hostname):$(basename $GN2_BASE_DIR)
 
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 1ef2bc26..1e66e957 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -82,6 +82,7 @@ assert_writable_dir(GENERATED_TEXT_DIR)
 # Flat file directories
 GENODIR              = flat_files('genotype')+'/'
 assert_dir(GENODIR)
+assert_dir(GENODIR+'bimbam') # for gemma
 
 # JSON genotypes are OBSOLETE
 JSON_GENODIR         = flat_files('genotype/json')+'/'
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 57f97a81..e3fcd7c7 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -278,8 +278,4 @@ if os.environ.get('WQFLASK_OVERRIDES'):
             logger.debug(OVERRIDES)
 
 # assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData")
-# assert_dir(get_setting("JS_BIODALLIANCE"))
-# assert_file(get_setting("JS_BIODALLIANCE")+"/build/dalliance-all.js")
-# assert_file(get_setting("JS_BIODALLIANCE")+"/build/worker-all.js")
-# assert_dir(get_setting("JS_TWITTER_POST_FETCHER"))
 assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js")
-- 
cgit v1.2.3