From 6e4a01fbdf2ac72230346d6f474edaa56a623bfe Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 19 Apr 2015 10:40:15 +0000
Subject: pylmm: can now be called from GN2 without path set

---
 wqflask/wqflask/my_pylmm/pyLMM/lmm.py | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index 4e35a4ac..2a0c7fdc 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -19,7 +19,6 @@ from __future__ import absolute_import, print_function, division
 
 import sys
 import time
-# import argparse
 import uuid
 
 import numpy as np
@@ -977,6 +976,7 @@ def gn2_load_redis_iter(key,species,kinship,pheno,geno_iterator):
 # Note that this calling route will become OBSOLETE (we should use runlmm.py
 # instead)
 def gn2_main():
+    import argparse
     parser = argparse.ArgumentParser(description='Run pyLMM')
     parser.add_argument('-k', '--key')
     parser.add_argument('-s', '--species')
@@ -991,9 +991,5 @@ def gn2_main():
 
 if __name__ == '__main__':
     print("WARNING: Calling pylmm from lmm.py will become OBSOLETE, use runlmm.py instead!")
-    if has_gn2:
-        gn2_main()
-    else:
-        fatal("Run from runlmm.py instead")
-
+    gn2_main()
 
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