diff options
| -rwxr-xr-x | bin/genenetwork2 | 9 | ||||
| -rw-r--r-- | wqflask/base/data_set.py | 2 | ||||
| -rw-r--r-- | wqflask/runserver.py | 11 |
3 files changed, 16 insertions, 6 deletions
diff --git a/bin/genenetwork2 b/bin/genenetwork2 index 52d3155c..ff1146b6 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -1,5 +1,11 @@ #! /bin/bash # +# Typical usage +# +# env GN2_PROFILE=~/opt/genenetwork2-phewas ./bin/genenetwork2 +# +# Where GN2_PROFILE points to the GNU Guix profile used for deployment. +# # This will run the GN2 server (with default settings if none # supplied). Pass in your own settings file, e.g. # @@ -106,6 +112,9 @@ echo -n "dir $TMPDIR dbfilename gn2.rdb " | redis-server - & +# Overrides for packages that are not yet public (currently r-auwerx) +export R_LIBS_SITE=$R_LIBS_SITE:$HOME/.Rlibs/das1i1pm54dj6lbdcsw5w0sdwhccyj1a-r-3.3.2/lib/R/lib + # Start the flask server running GN2 cd $GN2_BASE_DIR/wqflask echo "Starting with $settings" diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 54dd3c4b..671657e8 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -328,7 +328,7 @@ class DatasetGroup(object): if check_plink_gemma(): marker_class = HumanMarkers else: - marker_class = Markers + marker_class = Markers self.markers = marker_class(self.name) diff --git a/wqflask/runserver.py b/wqflask/runserver.py index adacc712..40616223 100644 --- a/wqflask/runserver.py +++ b/wqflask/runserver.py @@ -19,16 +19,17 @@ ENDC = '\033[0m' import os app.config['SECRET_KEY'] = os.urandom(24) -from utility.tools import WEBSERVER_MODE,get_setting_int,get_setting +from utility.tools import WEBSERVER_MODE,get_setting_int,get_setting,get_setting_bool port = get_setting_int("SERVER_PORT") print("GN2 API server URL is ["+BLUE+get_setting("GN_SERVER_URL")+ENDC+"]") -import requests -page = requests.get(get_setting("GN_SERVER_URL")) -if page.status_code != 200: - raise Exception("API server not found!") +if get_setting_bool("USE_GN_SERVER"): + import requests + page = requests.get(get_setting("GN_SERVER_URL")) + if page.status_code != 200: + raise Exception("API server not found!") print("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % (BLUE,str(port),ENDC,get_setting("WEBSERVER_URL"))) |