support TRINITY_HOME or TRINITYHOME

Author: Jon Palmer

funannotate/__version__.py

@@ -1,3 +1,3 @@
-VERSION = (1, 7, 0)
+VERSION = (1, 7, 1)
 
 __version__ = '.'.join(map(str, VERSION))

funannotate/check.py

@@ -116,7 +116,7 @@ def check_version2(name):
             vers = subprocess.Popen(
                 [name, '--version'], stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()[1]
             vers = vers.strip()
-            vers = vers.split(': ')[-1]        	
+            vers = vers.split(': ')[-1]         
         elif name == 'emapper.py':
             vers = subprocess.Popen([name, '--version'], stdout=subprocess.PIPE).communicate()[
                 0].split('\n')[1].replace('emapper-', '')
@@ -365,7 +365,15 @@ def main(args):
             if show:
                 print('$%s=%s' % (var, VARI))
         except KeyError:
-            missing.append(var)
+            if var == 'TRINITYHOME':
+                try:
+                    VARI = os.environ['TRINITY_HOME']
+                    if show:
+                        print('$%s=%s' % ('TRINITY_HOME', VARI))
+                except KeyError:
+                    missing.addend(var)             
+            else:
+                missing.append(var)
             pass
     if len(missing) > 0:
         for x in missing:

funannotate/train.py

@@ -689,9 +689,12 @@ def __init__(self, prog):
         try:
             TRINITY = os.environ["TRINITYHOME"].strip()
         except KeyError:
-            lib.log.error(
-                "$TRINITYHOME environmental variable not found, TRINITY is not properly configured. You can use the --TRINITYHOME argument to specify a path at runtime.")
-            sys.exit(1)
+        	try:
+        		TRINITY = os.environ["TRINITY_HOME"].strip()
+        	except KeyError:
+				lib.log.error(
+					"$TRINITYHOME nor $TRINITY_HOME environmental variable not found, TRINITY is not properly configured. You can use the --TRINITYHOME argument to specify a path at runtime.")
+				sys.exit(1)
     else:
         TRINITY = args.TRINITYHOME.strip()
 

funannotate/update.py

@@ -1638,9 +1638,12 @@ def __init__(self, prog):
         try:
             TRINITY = os.environ["TRINITYHOME"].strip()
         except KeyError:
-            lib.log.error(
-                "$TRINITYHOME environmental variable not found, TRINITY is not properly configured. You can use the --TRINITYHOME argument to specify a path at runtime.")
-            sys.exit(1)
+        	try:
+        		TRINITY = os.environ["TRINITY_HOME"].strip()
+        	except KeyError:
+				lib.log.error(
+					"$TRINITYHOME nor $TRINITY_HOME environmental variable not found, TRINITY is not properly configured. You can use the --TRINITYHOME argument to specify a path at runtime.")
+				sys.exit(1)
     else:
         TRINITY = args.TRINITYHOME.strip()