diff options
| -rwxr-xr-x | bin/genenetwork2 | 2 | ||||
| -rw-r--r-- | etc/default_settings.py | 4 | ||||
| -rw-r--r-- | wqflask/utility/tools.py | 2 |
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()) |