reset LD_LIBRARY_PATH when calling external programs

davidemms · Nov 25, 2016 · 692122e · 692122e
1 parent cbacdb5
commit 692122e
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Showing 3 changed files with 28 additions and 6 deletions.
diff --git a/orthofinder/orthofinder.py b/orthofinder/orthofinder.py
@@ -55,10 +55,17 @@
     with open(os.devnull, "w") as f:
         subprocess.call("taskset -p 0xffffffffffff %d" % os.getpid(), shell=True, stdout=f) # get round problem with python multiprocessing library that can set all cpu affinities to a single cpu
 
+# Fix LD_LIBRARY_PATH when using pyinstaller 
 my_env = os.environ.copy()
 if getattr(sys, 'frozen', False):
-#    my_env['LD_LIBRARY_PATH'] = my_env['LD_LIBRARY_PATH_ORIG']  
-    my_env['LD_LIBRARY_PATH'] = ''        
+    if 'LD_LIBRARY_PATH_ORIG' in my_env:
+        my_env['LD_LIBRARY_PATH'] = my_env['LD_LIBRARY_PATH_ORIG']  
+    else:
+        my_env['LD_LIBRARY_PATH'] = ''  
+    if 'DYLD_LIBRARY_PATH_ORIG' in my_env:
+        my_env['DYLD_LIBRARY_PATH'] = my_env['DYLD_LIBRARY_PATH_ORIG']  
+    else:
+        my_env['DYLD_LIBRARY_PATH'] = ''      
 
 def RunBlastDBCommand(command):
     capture = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, env=my_env)

diff --git a/orthofinder/scripts/get_orthologues.py b/orthofinder/scripts/get_orthologues.py
@@ -48,10 +48,18 @@
 import blast_file_processor as BlastFileProcessor
 
 nThreads = util.nThreadsDefault
+
+# Fix LD_LIBRARY_PATH when using pyinstaller 
 my_env = os.environ.copy()
 if getattr(sys, 'frozen', False):
-#    my_env['LD_LIBRARY_PATH'] = my_env['LD_LIBRARY_PATH_ORIG']  
-    my_env['LD_LIBRARY_PATH'] = ''  
+    if 'LD_LIBRARY_PATH_ORIG' in my_env:
+        my_env['LD_LIBRARY_PATH'] = my_env['LD_LIBRARY_PATH_ORIG']  
+    else:
+        my_env['LD_LIBRARY_PATH'] = ''  
+    if 'DYLD_LIBRARY_PATH_ORIG' in my_env:
+        my_env['DYLD_LIBRARY_PATH'] = my_env['DYLD_LIBRARY_PATH_ORIG']  
+    else:
+        my_env['DYLD_LIBRARY_PATH'] = ''     
 
 class Seq(object):
     def __init__(self, seqInput):

diff --git a/orthofinder/scripts/util.py b/orthofinder/scripts/util.py
@@ -49,10 +49,17 @@
 picProtocol = 1
 version = "1.1.2"
 
+# Fix LD_LIBRARY_PATH when using pyinstaller 
 my_env = os.environ.copy()
 if getattr(sys, 'frozen', False):
-#    my_env['LD_LIBRARY_PATH'] = my_env['LD_LIBRARY_PATH_ORIG']  
-    my_env['LD_LIBRARY_PATH'] = ""  
+    if 'LD_LIBRARY_PATH_ORIG' in my_env:
+        my_env['LD_LIBRARY_PATH'] = my_env['LD_LIBRARY_PATH_ORIG']  
+    else:
+        my_env['LD_LIBRARY_PATH'] = ''  
+    if 'DYLD_LIBRARY_PATH_ORIG' in my_env:
+        my_env['DYLD_LIBRARY_PATH'] = my_env['DYLD_LIBRARY_PATH_ORIG']  
+    else:
+        my_env['DYLD_LIBRARY_PATH'] = ''    
 
 def PrintNoNewLine(text):
     sys.stdout.write(text)