overwrite system temp directory for panaroo python instance to redirect gffutils temporary files

Author: gtonkinhill

panaroo/__init__.py

@@ -1,2 +1,2 @@
 '''An updated pipeline for pangenome investigation'''
-__version__ = '1.4.0'
+__version__ = '1.4.1'

panaroo/__main__.py

@@ -294,6 +294,7 @@ def main():
     args.output_dir = os.path.join(args.output_dir, "")
     # Create temporary directory
     temp_dir = os.path.join(tempfile.mkdtemp(dir=args.output_dir), "")
+    os.environ['TMPDIR'] = temp_dir
 
     # check if input is a file containing filenames
     if len(args.input_files) == 1:

panaroo/integrate.py

@@ -260,6 +260,7 @@ def main():
 
     # Create temporary directory
     temp_dir = os.path.join(tempfile.mkdtemp(dir=args.output_dir), "")
+    os.environ['TMPDIR'] = temp_dir
 
     directories = [args.input_dir, temp_dir]
 

panaroo/merge_graphs.py

@@ -596,6 +596,7 @@ def main():
 
     # create temporary directory
     temp_dir = os.path.join(tempfile.mkdtemp(dir=args.output_dir), "")
+    os.environ['TMPDIR'] = temp_dir
 
     # run the main merge script
     merge_graphs(directories=args.directories,

panaroo/run_prokka.py

@@ -107,6 +107,7 @@ def run_prokka_mod(input_file, out_folder, train_file, force, add_cmds):
     # Create temporary directory
     temp_dir = os.path.join(os.path.abspath(tempfile.mkdtemp(dir=out_folder)),
                             "")
+    os.environ['TMPDIR'] = temp_dir
     with open(temp_dir + "/prodigal", 'w') as outfile:
         outfile.write("#!/bin/bash\n")
         outfile.write("(>&2 echo 'running prokka mod!')\n")