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authorpjotrp2016-02-24 09:25:43 +0000
committerPjotr Prins2016-04-20 09:01:42 +0000
commit92fda7557645199276bf4f8a65c40252c4d83c21 (patch)
tree824940fb4a5a768128a8ba4d4a804558628f31d6
parente5951ad5f3bb244e4dc53cd04c291dcbdef544a0 (diff)
downloadgenenetwork2-92fda7557645199276bf4f8a65c40252c4d83c21.tar.gz
Settled on the _COMMAND syntax over _RUN
-rw-r--r--etc/default_settings.py6
-rw-r--r--wqflask/utility/tools.py10
2 files changed, 6 insertions, 10 deletions
diff --git a/etc/default_settings.py b/etc/default_settings.py
index 48d3f66b..6a218f26 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -24,6 +24,6 @@ SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a
# Path overrides for Genenetwork
GENENETWORK_FILES = "../../gn2_data"
-PYLMM_RUN = os.popen("which pylmm_redis").read()
-PLINK_RUN = os.popen("which plink2").read()
-GEMMA_RUN = os.popen("which gemma").read()
+PYLMM_COMMAND = os.popen("which pylmm_redis").read()
+PLINK_COMMAND = os.popen("which plink2").read()
+GEMMA_COMMAND = os.popen("which gemma").read()
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index d4c10c68..0f2e4d88 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -1,9 +1,5 @@
# Tools/paths finder resolves external paths from settings and/or environment
# variables
-#
-# Currently supported:
-#
-# PYLMM_PATH finds the root of the git repository of the pylmm_gn2 tool
import os
import sys
@@ -69,13 +65,13 @@ def valid_path(dir):
return None
def pylmm_command(guess=None):
- return valid_bin(get_setting("PYLMM_RUN",guess))
+ return valid_bin(get_setting("PYLMM_COMMAND",guess))
def gemma_command(guess=None):
- return valid_bin(get_setting("GEMMA_RUN",guess))
+ return valid_bin(get_setting("GEMMA_COMMAND",guess))
def plink_command(guess=None):
- return valid_bin(get_setting("PLINK_RUN",guess))
+ return valid_bin(get_setting("PLINK_COMMAND",guess))
def flat_files(subdir=None):
base = get_setting("GENENETWORK_FILES")