diff options
| -rwxr-xr-x | wqflask/wqflask/my_pylmm/pyLMM/lmm.py | 21 |
1 files changed, 15 insertions, 6 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py index 369fcbcc..8de3b3a7 100755 --- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py @@ -45,11 +45,16 @@ import sys sys.path.append("/home/zas1024/gene/wqflask/") print("sys.path2:", sys.path) -from utility.benchmark import Bench -from utility import temp_data - -from wqflask.my_pylmm.pyLMM import chunks +has_gn2=True +try: + from utility.benchmark import Bench + from utility import temp_data + from wqflask.my_pylmm.pyLMM import chunks +except ImportError: + print("WARNING: Standalone version\n") + has_gn2=False + pass #np.seterr('raise') @@ -288,6 +293,7 @@ def run_other(pheno_vector, def matrixMult(A,B): # If there is no fblas then we will revert to np.dot() + try: linalg.fblas except AttributeError: @@ -708,7 +714,7 @@ class LMM: pl.ylabel("Probability of data") pl.title(title) -def main(): +def gn2_main(): parser = argparse.ArgumentParser(description='Run pyLMM') parser.add_argument('-k', '--key') parser.add_argument('-s', '--species') @@ -750,7 +756,10 @@ def main(): Redis.expire(results_key, 60*60) if __name__ == '__main__': - main() + if has_gn2: + gn2_main() + else: + cli_main() |