Fix bug: Cluster execution does not work within a virtual environment

psot/config.py

@@ -105,6 +105,11 @@ class Config:
       config['install_path'] = pkg_resources.resource_filename('psot', '')
       config['helpers_path'] = pkg_resources.resource_filename('psot', 'helpers')
       config['repository_paths'] = self.repo_paths
+
+      # check if running inside a virtual environment
+      if 'VIRTUAL_ENV' in os.environ:
+        config['venv'] = os.environ['VIRTUAL_ENV']
+
       self.merge_modules_in_profiles(config)
       return config
 

psot/main.py

@@ -67,6 +67,8 @@ def generate_execution(config, args):
     execution['fasta'] = os.path.abspath(args.fasta)
     execution['output'] = os.path.abspath(args.output)
     execution['install_path'] = config['install_path']
+    if 'venv' in config:
+        execution['venv'] = config['venv']
     if args.execution_dir:
         execution['directory'] = os.path.abspath(args.execution_dir)
     else:

psot/nextflow.py

@@ -191,6 +191,8 @@ Channel.fromPath(params.fasta).set{fasta}''')
             config['executor'] = 'sge'
             config['chunks'] = ".splitFasta(by:300, file:'input')"
             config['clusterOptions'] = "clusterOptions='-S /bin/bash'"
+            if 'venv' in execution:
+              config['clusterOptions'] = config['clusterOptions'] + "\nbeforeScript 'export PS1=; source " + execution['venv'] + "/bin/activate'"
         else:
             config['executor'] = 'local'
             config['chunks'] = ''