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authorPjotr Prins2016-04-20 08:49:59 +0000
committerPjotr Prins2016-04-20 08:49:59 +0000
commit3be9e4a0950b1ea2d560463032c6f4104baf738e (patch)
tree2b976ee9d78e2235121954f19ea1fa7d0f913426 /wqflask
parent94e3ac8e2fff5da72fd1c0358fdb6fdad9a7830c (diff)
downloadgenenetwork2-3be9e4a0950b1ea2d560463032c6f4104baf738e.tar.gz
[PATCH 026/100] Introducing cached values PYLMM_COMMAND,
GEMMA_COMMAND, PLINK_COMMAND and TEMPDIR
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/utility/tools.py8
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression.py11
2 files changed, 8 insertions, 11 deletions
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index dc7bc33c..5d69e699 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -81,4 +81,10 @@ def flat_files(subdir=None):
def tempdir():
return valid_path(get_setting("TEMPDIR","/tmp"))
-TEMPDIR = tempdir()
+# Cached values
+
+PYLMM_COMMAND = pylmm_command()
+GEMMA_COMMAND = pylmm_command()
+PLINK_COMMAND = pylmm_command()
+FLAT_FILES = flat_files()
+TEMPDIR = tempdir()
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index b0f5ed69..a76a5967 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -36,21 +36,12 @@ from utility import helper_functions
from utility import Plot, Bunch
from utility import temp_data
from utility.benchmark import Bench
-from utility.tools import pylmm_command, plink_command, gemma_command
from wqflask.marker_regression import gemma_mapping
#from wqflask.marker_regression import qtl_reaper_mapping
#from wqflask.marker_regression import plink_mapping
#from wqflask.marker_regression import rqtl_mapping
-# Check for valid binary paths of pylmm, plink, rqtl etc. This code
-# runs at startup, so a missing binary will balk before running the
-# service
-
-GEMMA_RUN = gemma_command()
-PYLMM_RUN = pylmm_command()
-PLINK_RUN = plink_command()
-# RQTL_PATH,RQTL_COMMAND = rqtl_command()
-
+from utility.tools import PYLMM_COMMAND, GEMMA_COMMAND, PLINK_COMMAND
class MarkerRegression(object):