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| author | Lei Yan | 2017-06-26 19:40:09 +0000 |
|---|---|---|
| committer | Lei Yan | 2017-06-26 19:40:09 +0000 |
| commit | 10e3996ad0f1da29dd6f27ec3c10aa6d8660ed03 (patch) | |
| tree | 59eba8bb4f99087854d6004648023b05e0a69b38 /etc | |
| parent | afd2028e0ddab64e433eceb19e8cbd8d7149e080 (diff) | |
| parent | e467c3f19824415d9e9a3fdd4073d44439c83cbf (diff) | |
| download | genenetwork2-10e3996ad0f1da29dd6f27ec3c10aa6d8660ed03.tar.gz | |
Merge branch 'master' of github.com:genenetwork/genenetwork2
Diffstat (limited to 'etc')
| -rw-r--r-- | etc/VERSION | 1 | ||||
| -rw-r--r-- | etc/default_settings.py | 33 |
2 files changed, 19 insertions, 15 deletions
diff --git a/etc/VERSION b/etc/VERSION new file mode 100644 index 00000000..1785aa28 --- /dev/null +++ b/etc/VERSION @@ -0,0 +1 @@ +2.10rc3 diff --git a/etc/default_settings.py b/etc/default_settings.py index 6acea637..1b609414 100644 --- a/etc/default_settings.py +++ b/etc/default_settings.py @@ -9,6 +9,8 @@ # env LOG_SQL=True USE_REDIS=False ./bin/genenetwork2 # env LOG_LEVEL=DEBUG ./bin/genenetwork2 ~/gn2_settings.py # +# Typically you need to set GN2_PROFILE too. +# # Note also that in the near future we will additionally fetch # settings from a JSON file # @@ -18,10 +20,9 @@ import os import sys -GN_VERSION = open("../VERSION","r").read() +GN_VERSION = open("../etc/VERSION","r").read() SQL_URI = "mysql://gn2:mysql_password@localhost/db_webqtl_s" -SQLALCHEMY_DATABASE_URI = 'mysql://gn2:mysql_password@localhost/db_webqtl_s' -SQLALCHEMY_POOL_RECYCLE = 3600 +SQL_ALCHEMY_POOL_RECYCLE = 3600 GN_SERVER_URL = "http://localhost:8880/" # ---- Flask configuration (see website) @@ -45,24 +46,26 @@ WEBSERVER_DEPLOY = None # Deployment specifics (nyi) LOG_LEVEL = 'WARNING' # Logger mode (DEBUG|INFO|WARNING|ERROR|CRITICAL) LOG_LEVEL_DEBUG = '0' # logger.debugf log level (0-5, 5 = show all) LOG_SQL = 'False' # Log SQL/backend and GN_SERVER calls -LOG_SQLALCHEMY = 'False' +LOG_SQL_ALCHEMY = 'False' LOG_BENCH = True # Log bench marks USE_REDIS = True # REDIS caching (note that redis will be phased out) USE_GN_SERVER = 'False' # Use GN_SERVER SQL calls +HOME = os.environ['HOME'] -# Paths to JS libraries +# ---- Default locations +GENENETWORK_FILES = HOME+"/gn2_data" # base dir for all static data files -TWITTER_POST_FETCHER_JS_PATH = os.environ['HOME']+"/genenetwork/Twitter-Post-Fetcher" +# ---- Path overrides for Genenetwork - the defaults are normally +# picked up from Guix or in the HOME directory -# ---- Path overrides for Genenetwork # TMPDIR is normally picked up from the environment -HOME=os.environ['HOME'] -LOGFILE = HOME+"/genenetwork2.log" -GENENETWORK_FILES = HOME+"/gn2_data" # base dir for all static data files -LOCAL_PRIVATE_FILES = HOME+"/gn2_private_data" # private static data files +# PRIVATE_FILES = HOME+"/gn2_private_data" # private static data files (unused) + +# ---- Local path to JS libraries - for development modules (only) +JS_GN_PATH = os.environ['HOME']+"/genenetwork/javascript" -# ---- GN2 Executables -PYLMM_COMMAND = str.strip(os.popen("which pylmm_redis").read()) -PLINK_COMMAND = str.strip(os.popen("which plink2").read()) -GEMMA_COMMAND = str.strip(os.popen("which gemma").read()) +# ---- GN2 Executables (overwrite for testing only) +# PYLMM_COMMAND = str.strip(os.popen("which pylmm_redis").read()) +# PLINK_COMMAND = str.strip(os.popen("which plink2").read()) +# GEMMA_COMMAND = str.strip(os.popen("which gemma").read()) |