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authorzsloan2017-06-02 16:38:11 +0000
committerzsloan2017-06-02 16:38:11 +0000
commit87d409765773c32ba4f53aede5dbc1e54bddadae (patch)
tree302936e68747a7dfa476bfcdf75cdbf967c9be08
parentd778dc2ff9031d2c271764fc3b033b794e29ac10 (diff)
parente467c3f19824415d9e9a3fdd4073d44439c83cbf (diff)
downloadgenenetwork2-87d409765773c32ba4f53aede5dbc1e54bddadae.tar.gz
Merge branch 'master' of github.com:genenetwork/genenetwork2 into development
-rwxr-xr-xbin/genenetwork22
-rw-r--r--etc/default_settings.py4
-rw-r--r--wqflask/utility/tools.py2
3 files changed, 5 insertions, 3 deletions
diff --git a/bin/genenetwork2 b/bin/genenetwork2
index b3190f1e..236d8f63 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -74,7 +74,7 @@ else
export XDG_DATA_DIRS="$GN2_PROFILE/share"
export GIO_EXTRA_MODULES="$GN2_PROFILE/lib/gio/modules"
export LC_ALL=C # FIXME
- export GENENETWORK_FILES="$GN2_PROFILE/share/genenetwork2"
+ export GUIX_GENENETWORK_FILES="$GN2_PROFILE/share/genenetwork2"
export PLINK_COMMAND="$GN2_PROFILE/bin/plink2"
export PYLMM_COMMAND="$GN2_PROFILE/bin/pylmm_redis"
export GEMMA_COMMAND="$GN2_PROFILE/bin/gemma"
diff --git a/etc/default_settings.py b/etc/default_settings.py
index 1c5b10b4..1b609414 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -53,11 +53,13 @@ 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']
+# ---- Default locations
+GENENETWORK_FILES = HOME+"/gn2_data" # base dir for all static data files
+
# ---- Path overrides for Genenetwork - the defaults are normally
# picked up from Guix or in the HOME directory
# TMPDIR is normally picked up from the environment
-# GENENETWORK_FILES = HOME+"/gn2_data" # base dir for all static data files
# PRIVATE_FILES = HOME+"/gn2_private_data" # private static data files (unused)
# ---- Local path to JS libraries - for development modules (only)
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 49e3471e..393ff2df 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -233,7 +233,7 @@ GENENETWORK_FILES = get_setting('GENENETWORK_FILES')
JS_GUIX_PATH = get_setting('JS_GUIX_PATH')
# assert_dir(JS_GUIX_PATH) - don't enforce right now
JS_GN_PATH = get_setting('JS_GN_PATH')
-assert_dir(JS_GN_PATH)
+# assert_dir(JS_GN_PATH)
PYLMM_COMMAND = app_set("PYLMM_COMMAND",pylmm_command())
GEMMA_COMMAND = app_set("GEMMA_COMMAND",gemma_command())