add download_databases function to main.py,...

add download_databases function to main.py, download_databases_from_s3bucket.sh is run as subprocess

psot/main.py

 #!/usr/bin/env python3
 import argparse
 import os
-from psot.config import load_config
+import subprocess
 import copy
 import shutil
-from psot.nextflow import setup_execution_directory, execute_analysis
 import tempfile
 import sys
 import json
+from psot.config import load_config
+from psot.nextflow import setup_execution_directory, execute_analysis
+
 
 def main():
     parser = argparse.ArgumentParser(description='Make bioinformatic observations on aminoacid sequences')
@@ -54,6 +56,7 @@ def analyze(args, config):
     execution = generate_execution(config, args)
     if args.debug:
         print(json.dumps(execution, indent=2))
+    download_databases(execution)
     setup_execution_directory(execution)
     error_code = execute_analysis(execution)
     cleanup(execution)
@@ -129,5 +132,19 @@ def show_analyses(config):
         module = config['modules'][key]
         print('   {0:<20} - {1}'.format(module['name'], module['info']))
 
+def download_databases(execution):
+    
+    script = execution['helpers_path'] + '/download_databases_from_s3bucket.sh'
+    logfile = execution['install_path'] + '/database_paths.log'
+    database_path = execution['database_path']
+    
+    retcode = 1 
+    try:
+        run_download_script = subprocess.run([script, logfile, database_path])
+        retcode = run_download_script.returncode
+    except OSError as e:
+        print("Execution failed:", e, file=sys.stderr)
+    return retcode
+
 if __name__ == "__main__":
     main()

psot/nextflow.py

@@ -342,17 +342,17 @@ def generate_nextflow_config(execution):
     fragments = []
     
     if execution['docker']:
-        fragments.append('''docker {
+        fragments.append('''docker {{
             enabled = 'true'
             fixOwnership = 'true'
-            runOptions = '--volume={path}/databases'
-        }
+            runOptions = '--volume={path}:/databases'
+        }}
         '''.format(path=database_path))
     elif execution['singularity']:
-        fragments.append('''singularity {
+        fragments.append('''singularity {{
             enabled = 'true'
             runOptions = '--bind {path}:/databases'
-        }
+        }}
         '''.format(path=database_path))
         
     fragments.append('''process { ''')