fix path access and parse errors

maxplanck-ie · Nov 6, 2017 · 669774d · 669774d
1 parent 07a4b7d
commit 669774d
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Showing 5 changed files with 49 additions and 321 deletions.
diff --git a/README.md b/README.md
diff --git a/workflows/ChIP-seq/ChIP-seq b/workflows/ChIP-seq/ChIP-seq
@@ -29,8 +29,8 @@ import yaml
 import inspect
 
 
-#sys.path.append(os.path.abspath(inspect.getfile(inspect.currentframe())) + "../../shared/")
-sys.path.append(os.path.join(os.path.dirname(os.path.dirname(os.path.dirname(inspect.getfile(inspect.currentframe())))))+"/shared/")
+sys.path.append(os.path.abspath(os.path.dirname(inspect.getfile(inspect.currentframe()))) + "/shared/")
+#sys.path.append(os.path.join(os.path.dirname(os.path.dirname(os.path.dirname(inspect.getfile(inspect.currentframe())))))+"/shared/")
 
 
 import common_functions as cf
@@ -139,11 +139,21 @@ def parse_args(defaults={"verbose":None,"configfile":None,"max_jobs":None,"snake
 
 def main():
 
+    ## basic paths only used in wrapper
+    #this_script_dir = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))
+    this_script_dir = os.path.dirname(os.path.realpath(__file__))
+    main_dir_path = os.path.join(os.path.dirname(os.path.dirname(this_script_dir)))
+
     ## defaults
     defaults = cf.load_configfile(os.path.join(this_script_dir, "defaults.yaml"),False)
 
     ## get command line arguments
-    args = parser.parse_args(defaults)
+    parser = parse_args(defaults)
+    args = parser.parse_args()
+
+    ## we also add these paths to config, although we dont use them in the Snakefile
+    args.this_script_dir = this_script_dir
+    args.main_dir_path = main_dir_path
 
     ## checks for parameters necessary in wrapper
 # 1. Dir path
@@ -173,16 +183,6 @@ def main():
             print("\nSample info file not found! (--DB {})\n".format(args.sample_info))
             exit(1)
 
-
-    ## basic paths only used in wrapper
-    #this_script_dir = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))
-    this_script_dir = os.path.dirname(os.path.realpath(__file__))
-    main_dir_path = os.path.join(os.path.dirname(os.path.dirname(this_script_dir)))
-
-    ## we also add these paths to config, although we dont use them in the Snakefile
-    args.this_script_dir = this_script_dir
-    args.main_dir_path = main_dir_path
-
     ## merge configuration dicts
     config = defaults   # 1) form defaults.yaml
     if args.configfile:

diff --git a/workflows/DNA-mapping/DNA-mapping b/workflows/DNA-mapping/DNA-mapping
@@ -24,7 +24,8 @@ import yaml
 import inspect
 
 #sys.path.append(os.path.join(os.path.dirname(os.path.dirname(os.path.dirname(os.path.realpath('__file__')))))+"/shared/")
-sys.path.append(os.path.abspath(inspect.getfile(inspect.currentframe())) + "../../shared/")
+sys.path.append(os.path.abspath(os.path.dirname(inspect.getfile(inspect.currentframe()))) + "/shared/")
+
 import common_functions as cf
 
 
@@ -220,11 +221,19 @@ def parse_args(defaults={"verbose":None,"configfile":None,"max_jobs":None,"snake
 
 def main():
 
+    ## basic paths only used in wrapper
+    this_script_dir = os.path.dirname(os.path.realpath(__file__))
+    main_dir_path = os.path.join(os.path.dirname(os.path.dirname(this_script_dir)))
+
     ## defaults
     defaults = cf.load_configfile(os.path.join(this_script_dir, "defaults.yaml"),False)
 
     ## get command line arguments
-    args = parser.parse_args(defaults)
+    parser = parse_args(defaults)
+    args = parser.parse_args()
+    ## we also add these paths to config, although we dont use them in the Snakefile
+    args.this_script_dir = this_script_dir
+    args.main_dir_path = main_dir_path
 
     args.outdir = os.path.abspath(args.outdir)
     args.cluster_logs_dir = os.path.join(args.outdir, "cluster_logs")
@@ -249,15 +258,6 @@ def main():
         print("\nError! Provided configfile (-c) not found! ({})\n".format(args.configfile))
         exit(1)
 
-
-    ## basic paths only used in wrapper
-    this_script_dir = os.path.dirname(os.path.realpath(__file__))
-    main_dir_path = os.path.join(os.path.dirname(os.path.dirname(this_script_dir)))
-
-    ## we also add these paths to config, although we dont use them in the Snakefile
-    args.this_script_dir = this_script_dir
-    args.main_dir_path = main_dir_path
-
     ## merge configuration dicts
     config = defaults   # 1) form defaults.yaml
     if args.configfile: