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authorPjotr Prins2017-12-20 10:02:43 -0600
committerPjotr Prins2017-12-20 10:02:43 -0600
commit8ae775f831c278a3ad97372ad90cba5845e8e6ca (patch)
tree71f61ba9cd61c73206e581d21e426f4f599b3a51 /wqflask/utility/tools.py
parent837ce8b9c779b1da6e4390220ccd353b289c1fca (diff)
downloadgenenetwork2-8ae775f831c278a3ad97372ad90cba5845e8e6ca.tar.gz
tools: find path for JS and gemma_wrapper
Diffstat (limited to 'wqflask/utility/tools.py')
-rw-r--r--wqflask/utility/tools.py17
1 files changed, 9 insertions, 8 deletions
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 63b7149c..57f97a81 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -105,7 +105,7 @@ def js_path(module=None):
try_guix = get_setting("JS_GUIX_PATH")+"/"+module
if valid_path(try_guix):
return try_guix
- raise "No JS path found for "+module+" (check JS_GN_PATH)"
+ raise "No JS path found for "+module+" (if not in Guix check JS_GN_PATH)"
def pylmm_command(guess=None):
return assert_bin(get_setting("PYLMM_COMMAND",guess))
@@ -247,13 +247,14 @@ USE_GN_SERVER = get_setting_bool('USE_GN_SERVER')
GENENETWORK_FILES = get_setting('GENENETWORK_FILES')
JS_GUIX_PATH = get_setting('JS_GUIX_PATH')
-# assert_dir(JS_GUIX_PATH) - don't enforce right now
+assert_dir(JS_GUIX_PATH)
JS_GN_PATH = get_setting('JS_GN_PATH')
# assert_dir(JS_GN_PATH)
PYLMM_COMMAND = app_set("PYLMM_COMMAND",pylmm_command())
GEMMA_COMMAND = app_set("GEMMA_COMMAND",gemma_command())
PLINK_COMMAND = app_set("PLINK_COMMAND",plink_command())
+GEMMA_WRAPPER_COMMAND = gemma_wrapper_command()
TEMPDIR = tempdir() # defaults to UNIX TMPDIR
assert_dir(TEMPDIR)
@@ -276,9 +277,9 @@ if os.environ.get('WQFLASK_OVERRIDES'):
OVERRIDES[k] = cmd
logger.debug(OVERRIDES)
-assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData")
-assert_dir(get_setting("JS_BIODALLIANCE"))
-assert_file(get_setting("JS_BIODALLIANCE")+"/build/dalliance-all.js")
-assert_file(get_setting("JS_BIODALLIANCE")+"/build/worker-all.js")
-assert_dir(get_setting("JS_TWITTER_POST_FETCHER"))
-assert_file(get_setting("JS_TWITTER_POST_FETCHER")+"/js/twitterFetcher_min.js")
+# assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData")
+# assert_dir(get_setting("JS_BIODALLIANCE"))
+# assert_file(get_setting("JS_BIODALLIANCE")+"/build/dalliance-all.js")
+# assert_file(get_setting("JS_BIODALLIANCE")+"/build/worker-all.js")
+# assert_dir(get_setting("JS_TWITTER_POST_FETCHER"))
+assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js")