Added configuration file for the whole system

bin/module_signalp.py

 #!/usr/bin/env python3
 import argparse
+import yaml
+import os
 from os import system
 
+def get_config_file():
+    """Finds the config file, that is located in the directory above script"""
+    script_path = os.path.realpath(__file__)
+    script_dir = os.path.dirname(script_path)
+    config_dir = os.path.dirname(script_dir)
+    config_file = os.path.join(config_dir, 'config.yaml')
+    return config_file
+
+def get_signalp_tool():
+    """Extracts the configuration entry for signalp. If it is not present, it defaults to signalp"""
+    tool = None
+    with open(get_config_file()) as f: 
+        config = yaml.load(f)
+        tool = config['tools'].get('signalp', 'signalp')
+    return tool
+
+
 parser = argparse.ArgumentParser(description='Find signal peptides in amino acid sequences')
 parser.add_argument('--fasta', '-f', required=True, help='A fasta file with aminoacid sequences')
 parser.add_argument('--organism', '-o', choices=['euk', 'gram+', 'gram-'], default='euk', help='The organism type')
 args = parser.parse_args()
 
-system("/vol/biotools/bin/signalp -t " + args.organism + " " + args.fasta)
+system(get_signalp_tool() + " -t " + args.organism + " " + args.fasta)

config.yaml

+tools:
+    signalp: '/vol/biotools/bin/signalp'