Updated executable loading so that it doesn't rely on wrapper scripts.

chipathlon/conf.py

@@ -40,6 +40,14 @@ peak_tools = [
     "music"
 ]
 
+executables = [
+    "bedtools",
+    "bamtools",
+    "samtools",
+    "idr",
+    "picard"
+] + align_tools + peak_tools
+
 # Peak_type validation
 peak_types = {
     "spp": ["narrow", "broad"],

chipathlon/pegasus_config.py

@@ -51,6 +51,11 @@ class PegasusConfig(object):
         """
         self._validate_notify()
         self._validate_sites()
+        if "install_paths" in self.config:
+            if len(self.config["install_paths"]) < 0:
+                self.errors.append("Error parsing config template file '%s': At least 1 install_path needs to be specified." % (self.config_file,))
+        else:
+            self.errors.append("Error parsing config template file '%s': install_paths must be included." % (self.config_file,))
         return
 
     def _validate_sites(self):

scripts/chip-gen

@@ -12,7 +12,7 @@ parser.add_argument("-d", "--dir", dest="dir", required=True, help="Directory na
 parser.add_argument("--param", dest="param", required=True, help="Path to param file to load.")
 parser.add_argument("--conf", dest="config", required=True, help="Path to config file to load.")
 parser.add_argument("--run", dest="run", required=True, help="Path to run file to load.")
-parser.add_argument("--execute-sites", dest="execute_sites", required=True, nargs="+", default=["local"], help="List of execute sites.  Sites should be defined in configuration.")
+parser.add_argument("--execute-sites", dest="execute_sites", required=True, default="local", help="Target execute site.  Sites should be defined in configuration.")
 parser.add_argument("--output-site", dest="output_site", required=True, default="local", help="Target output site.  Site should be defined in configuration.")
 
 parser.add_argument("--rewrite", dest="rewrite", default=False, action="store_true", help="If specified, don't load from the database, rewrite files.")