use default python

Author: yunfeiguo

utils.py

@@ -13,6 +13,7 @@
 JAVA_XMX = "-Xmx"
 DEFAULT_JAVA = os.path.realpath(os.path.join(MY_DIR, "opt",
                                 "jdk1.8.0_131", "bin", "java"))
+DEFAULT_PYTHON = os.path.realpath(os.path.join(MY_DIR, "opt", "miniconda2", "bin", "python"))
 COMBINE_KEEP_ALL_DUPLICATE = 1
 COMBINE_KEEP_FIRST_DUPLICATE = 2
 COMBINE_KEEP_NO_DUPLICATE = 3
@@ -25,6 +26,14 @@ def get_java(java = "java"):
         return DEFAULT_JAVA
     return java
 
+def get_python(python = "python"):
+    '''
+    return default python if it exists
+    '''
+    if os.path.isfile(DEFAULT_PYTHON):
+        return DEFAULT_PYTHON
+    return python
+
 def count_variants(vcf):
     '''
     count number of variants

varsim_somatic.py

@@ -52,6 +52,7 @@ def varsim_somatic_main():
     main_parser.add_argument("--keep_temp", action="store_true", help="Keep temporary files")
     main_parser.add_argument("--java_max_mem", metavar="XMX", help="max java memory", default="10g", type = str)
     main_parser.add_argument("--java", metavar="PATH", help="path to java", default="java", type = str)
+    main_parser.add_argument("--python", metavar="PATH", help="path to python", default="python", type = str)
     main_parser.add_argument('--version', action='version', version=get_version())
 
 
@@ -178,7 +179,8 @@ def varsim_somatic_main():
     elif args.simulator == "art" and args.art_options:
         other_varsim_opts += ["--art_options", args.art_options]
 
-    varsim_command = ["python", os.path.realpath(VARSIM_PY),
+    args.python = utils.get_python(args.python)
+    varsim_command = [args.python, os.path.realpath(VARSIM_PY),
                       "--out_dir", str(os.path.realpath(args.out_dir)),
                       "--work_dir", str(os.path.realpath(args.work_dir)),
                       "--log_dir", str(os.path.realpath(os.path.join(args.log_dir, "varsim"))),