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| author | Pjotr Prins | 2016-03-03 11:21:01 +0000 |
|---|---|---|
| committer | Pjotr Prins | 2016-04-20 10:00:15 +0000 |
| commit | a66858e99c2195d90a187899db6f4dd8966a0a2c (patch) | |
| tree | e2c28be74e333614c78ef748ac8fdd165953effd | |
| parent | c52bf79ba92d2a632637536a9ea607c22ef2d9bf (diff) | |
| download | genenetwork2-a66858e99c2195d90a187899db6f4dd8966a0a2c.tar.gz | |
Show error when GENODIR is missing
| -rwxr-xr-x | bin/genenetwork2 | 13 | ||||
| -rw-r--r-- | etc/default_settings.py | 2 | ||||
| -rw-r--r-- | wqflask/utility/tools.py | 4 |
3 files changed, 10 insertions, 9 deletions
diff --git a/bin/genenetwork2 b/bin/genenetwork2 index a0a013fc..bbb2a19f 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -9,18 +9,19 @@ SCRIPT=$(readlink -f "$0") # Absolute path this script is in, thus /home/user/bin GN2_BASE_PATH=$(dirname $(dirname "$SCRIPT")) + +GN2_GUIX_PATH=$GN2_BASE_PATH/lib/python2.7/site-packages/genenetwork2-2.0-py2.7.egg +if [ -d $GN2_GUIX_PATH ]; then + GN2_BASE_PATH=$GN2_GUIX_PATH +fi echo $GN2_BASE_PATH # Handle settings parameter settings=$1 if [ -z $settings ]; then settings=$GN2_BASE_PATH/etc/default_settings.py ; fi if [ ! -e $settings ]; then - GN2_BASE_PATH=$GN2_BASE_PATH/lib/python2.7/site-packages/genenetwork2-2.0-py2.7.egg - settings=$GN2_BASE_PATH/etc/default_settings.py - if [ ! -e $settings ]; then - echo "ERROR: can not locate settings file - pass it in the command line" - exit 1 - fi + echo "ERROR: can not locate settings file - pass it in the command line" + exit 1 fi export WQFLASK_SETTINGS=$settings diff --git a/etc/default_settings.py b/etc/default_settings.py index 60a3a7b4..0cf40265 100644 --- a/etc/default_settings.py +++ b/etc/default_settings.py @@ -23,7 +23,7 @@ SERVER_PORT = 5003 SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a\xbc\xfc\x80:*\xebc' # Path overrides for Genenetwork -GENENETWORK_FILES = "../../gn2_data" +GENENETWORK_FILES = os.environ['HOME']+"/gn2_data" 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()) diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index b8eff12a..9405a9c6 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -76,8 +76,8 @@ def plink_command(guess=None): def flat_files(subdir=None): base = get_setting("GENENETWORK_FILES") if subdir: - return valid_path(base+"/"+subdir) - return valid_path(base) + return assert_dir(base+"/"+subdir) + return assert_dir(base) def assert_dir(dir): if not valid_path(dir): |