Moved helper scripts to own directory. Use absolute paths for scripts.

psot/config.py

@@ -66,8 +66,8 @@ class Repository:
                   module['analysis']['parameters'] = {}
               if module['converter']['parameters'] is None:
                   module['converter']['parameters'] = {}
-              module['analysis']['script'] = os.path.join(self.get_scripts_location(), module['analysis']['script'])
-              module['converter']['script'] = os.path.join(self.get_scripts_location(), module['converter']['script'])
+              module['analysis']['script'] = os.path.abspath(os.path.join(self.get_scripts_location(), module['analysis']['script']))
+              module['converter']['script'] = os.path.abspath(os.path.join(self.get_scripts_location(), module['converter']['script']))
       return modules
 
   def normalize_profiles(self, profiles):
@@ -120,6 +120,7 @@ class Config:
         config['app']['script_path'] = repo.get_scripts_location()
 
       config['install_path'] = pkg_resources.resource_filename('psot', '')
+      config['helpers_path'] = pkg_resources.resource_filename('psot', 'helpers')
       config['repository_paths'] = self.repo_paths
       return config
 
@@ -127,10 +128,14 @@ def load_config(repositories=None):
     # always use the installed repository as the first repo
     all_repositories = [pkg_resources.resource_filename('psot', '')]
 
+
     # check for repositories via environment variable
     if 'PSOT_REPOSITORIES' in os.environ:
       variable = os.environ['PSOT_REPOSITORIES']
       env_repos = variable.split(':')
+      # convert all paths to absolute paths
+      env_repos = [os.path.abspath(x) for x in env_repos]
+      os.environ['PSOT_REPOSITORIES'] = ":".join(env_repos)
       all_repositories.extend(env_repos) 
 
     if repositories:

psot/main.py

@@ -64,9 +64,9 @@ def generate_execution(config, args):
     execution['use_cluster'] = args.use_cluster
     execution['fetch_informations'] = args.fetch_informations 
     execution['mode'] = 'live' if args.live else 'complete'
-    execution['script_path'] = config['app']['script_path']
     execution['fasta'] = os.path.abspath(args.fasta)
     execution['output'] = os.path.abspath(args.output)
+    execution['install_path'] = config['install_path']
     if args.execution_dir:
         execution['directory'] = os.path.abspath(args.execution_dir)
     else:

psot/nextflow.py

@@ -166,7 +166,7 @@ def setup_execution_directory(execution):
         script_file.write(nextflow_script)
 
     if not os.path.exists(directory + '/bin'):
-        os.symlink(execution['script_path'], directory + '/bin')
+        os.symlink(os.path.join(execution['install_path'], 'helpers'), directory + '/bin')
     #if not os.path.exists(directory + '/psot'):
     #    os.symlink(execution['psot_path'], directory + '/psot')