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authorPjotr Prins2017-06-12 14:18:43 -0500
committerPjotr Prins2017-06-12 14:18:43 -0500
commitc81e466cb2284644d9d0bd7e1e668b30b79bc665 (patch)
treef0cf5d54c1a15a3a7620c36de9cbe9d1cb605b06 /wqflask/utility/tools.py
parentad7a2baa50e602c613fd4eba2f41cae7a2b75577 (diff)
downloadgenenetwork2-c81e466cb2284644d9d0bd7e1e668b30b79bc665.tar.gz
Fix binary paths for GEMMA_COMMAND, PYLMM_COMMAND and PLINK_COMMAND
Diffstat (limited to 'wqflask/utility/tools.py')
-rw-r--r--wqflask/utility/tools.py17
1 files changed, 11 insertions, 6 deletions
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 393ff2df..867bc5c8 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -108,13 +108,13 @@ def js_path(module=None):
raise "No JS path found for "+module+" (check JS_GN_PATH)"
def pylmm_command(guess=None):
- return valid_bin(get_setting("PYLMM_COMMAND",guess))
+ return assert_bin(get_setting("PYLMM_COMMAND",guess))
def gemma_command(guess=None):
- return valid_bin(get_setting("GEMMA_COMMAND",guess))
+ return assert_bin(get_setting("GEMMA_COMMAND",guess))
def plink_command(guess=None):
- return valid_bin(get_setting("PLINK_COMMAND",guess))
+ return assert_bin(get_setting("PLINK_COMMAND",guess))
def flat_file_exists(subdir):
base = get_setting("GENENETWORK_FILES")
@@ -126,6 +126,11 @@ def flat_files(subdir=None):
return assert_dir(base+"/"+subdir)
return assert_dir(base)
+def assert_bin(fn):
+ if not valid_bin(fn):
+ raise Exception("ERROR: can not find binary "+fn)
+ return fn
+
def assert_dir(dir):
if not valid_path(dir):
raise Exception("ERROR: can not find directory "+dir)
@@ -235,9 +240,9 @@ JS_GUIX_PATH = get_setting('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())
+PYLMM_COMMAND = pylmm_command()
+GEMMA_COMMAND = gemma_command()
+PLINK_COMMAND = plink_command()
TEMPDIR = tempdir() # defaults to UNIX TMPDIR
# ---- Handle specific JS modules