aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorPjotr Prins2018-02-10 07:53:53 +0000
committerPjotr Prins2018-02-10 07:53:53 +0000
commit97ccc478543a7bb08fe0cf178e320dd5811d8bfa (patch)
tree65c3610e421eea8615c377d922ad63d6cd258bde
parent4ae2d548127eeeaa7cec0baf1b788005b5e8e51d (diff)
downloadgenenetwork2-97ccc478543a7bb08fe0cf178e320dd5811d8bfa.tar.gz
Check for bimbam path and bail out if it is missing
-rwxr-xr-xbin/genenetwork21
-rw-r--r--wqflask/base/webqtlConfig.py1
-rw-r--r--wqflask/utility/tools.py4
3 files changed, 2 insertions, 4 deletions
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")