Merge pull request #5 from bewt85/bt5_more_javas

More javas

scripts/snpEffBuildAndRun

@@ -30,8 +30,6 @@ def parse_arguments():
   parser.add_argument('--keep', action='store_true', default=False,
                       help="Keep temporary files and databases (useful for debugging)")
   args = parser.parse_args()
-  args = check_and_amend_executables(args)
-
   return args
 
 if __name__ == '__main__':
@@ -43,4 +41,5 @@ if __name__ == '__main__':
     logging.basicConfig(format="[%(asctime)s] %(levelname)s: %(message)s",
                         level=logging.INFO)
   logger = logging.getLogger('snpEffWrapper')
+  args = check_and_amend_executables(args)
   annotate_vcf(args)

setup.py

@@ -3,7 +3,7 @@
 import multiprocessing
 
 setup(name='snpEffWrapper',
-      version='0.2.1',
+      version='0.2.2',
       scripts=[
         'scripts/snpEffBuildAndRun'
       ],

snpEffWrapper/wrapper.py

@@ -37,6 +37,8 @@ class AnnotationError(ValueError):
   pass
 
 def _java_version_ok(java):
+  if java is None:
+    return False
   try:
     output = subprocess.check_output([java, '-version'], stderr=subprocess.STDOUT)
     first_line = output.decode("utf-8").splitlines()[0]
@@ -48,14 +50,15 @@ def _java_version_ok(java):
     return False
 
 def _choose_java():
-  path_java = shutil.which('java')
-  if not path_java is None and _java_version_ok(path_java):
-    logger.debug("Using '%s'", path_java)
-    return path_java
-  sanger_pathogens_java='/software/pathogen/external/apps/usr/local/jdk1.7.0_21/bin/java'
-  if not path_java is None and _java_version_ok(sanger_pathogens_java):
-    logger.debug("Using '%s'", sanger_pathogens_java)
-    return sanger_pathogens_java
+  possible_javas = [
+    shutil.which('java'),
+    '/software/bin/java',
+    '/software/pathogen/external/apps/usr/local/jdk1.7.0_21/bin/java'
+  ]
+  for java in possible_javas:
+    if _java_version_ok(java):
+      logger.debug("Using '%s'", java)
+      return java
   raise WrongJavaError("Could not find a suitable version of Java (1.7)")
 
 def check_and_amend_executables(args):