Commit 59287112 authored by aknecht2's avatar aknecht2
Browse files

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

parent 33b5a5e9
......@@ -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"],
......
......@@ -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):
......
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......@@ -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.")
......
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