Added default execution in tmp directory

bin/nextflow.py

@@ -79,8 +79,10 @@ def setup_execution_directory(execution):
         os.symlink(execution['bin_path'], directory + '/bin')
 
 def execute_analysis(execution):
+    old_cwd = os.getcwd()
     os.chdir(execution['directory'])
-    os.system('nextflow run main.nf --fasta ' + execution['fasta'] + ' --output ' + execution['output'])
+    os.system('nextflow run ' + execution['directory'] + '/main.nf --fasta ' + execution['fasta'] + ' --output ' + execution['output'])
+    os.chdir(old_cwd)
 
 def generate_nextflow_script(execution):
     modules = execution['modules']

bin/psot

@@ -3,7 +3,9 @@ import argparse
 import os
 from config import load_config
 import copy
+import shutil
 from nextflow import setup_execution_directory, execute_analysis
+import tempfile
 
 def main():
     parser = argparse.ArgumentParser(description='Make bioinformatic observations on aminoacid sequences')
@@ -20,28 +22,40 @@ def main():
     analyze_parser.add_argument('--profile', '-p', default='fast', help='The profile to use')
     analyze_parser.add_argument('--live', '-l', action='store_true', help='Report results as they are computed, not only at the end of the computation')
     analyze_parser.add_argument('--config', '-c', help='The config to use')
+    analyze_parser.add_argument('--debug', '-d', action='store_true', help='Debug mode, computation directory will not be removed after computation')
+    analyze_parser.add_argument('--execution_dir', '-e', help='Use the specified execution directory and do not delete it after the computation')
     analyze_parser.set_defaults(func=analyze)
 
     args = parser.parse_args()
     config = load_config()
     args.func(args, config)
 
-
 def info(args, config):
     show_analyses(config)
 
 def analyze(args, config):
     execution = generate_execution(config, args)
+    if args.debug:
+        print(execution)
     setup_execution_directory(execution)
     execute_analysis(execution)
+    cleanup(execution)
+
+def cleanup(execution):
+    if not execution['debug']:
+        shutil.rmtree(execution['directory'])
 
 def generate_execution(config, args):
     execution = {}
+    execution['debug'] = args.debug
     execution['mode'] = 'live' if args.live else 'complete'
     execution['bin_path'] = config['app']['bin_path']
     execution['fasta'] = os.path.abspath(args.fasta)
     execution['output'] = os.path.abspath(args.output)
-    execution['directory'] = 'tmp' # TODO replace by random tmp directory or make it configurable (cli option)
+    if args.execution_dir:
+        execution['directory'] = args.execution_dir
+    else:
+        execution['directory'] = tempfile.mkdtemp()
     execution['modules'] = generate_execution_modules_for_profile(config, args.profile)
     return execution