From 1a76fca88178613e6faac558803199440d8d0f1a Mon Sep 17 00:00:00 2001
From: Yohan Jarosz <yohanjarosz@yahoo.fr>
Date: Tue, 21 Jul 2015 16:02:59 +0200
Subject: [PATCH] add --ask param
---
IMP | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/IMP b/IMP
index d356da8..4a3d6ea 100755
--- a/IMP
+++ b/IMP
@@ -16,7 +16,7 @@ __doc__ = """Integrated Metaomic Pipeline.
(____)(_/\/\_)(__)
Usage:
- IMP [-m MG1 -m MG2] [-t MT1 -t MT2] -o OUTPUT [--enter] [--norm] [-n CONTAINER] [-d DBPATH] [-e ENV] ... [COMMANDS ...]
+ IMP [-m MG1 -m MG2] [-t MT1 -t MT2] -o OUTPUT [--enter] [--norm] [--ask] [-n CONTAINER] [-d DBPATH] [-e ENV] ... [COMMANDS ...]
IMP --init [-d DBPATH]
IMP (-h | --help)
IMP --version
@@ -26,6 +26,7 @@ Options:
--enter Enter the container
--init Initialize IMP databases (Take a while)
--norm Don't delete the container after use. Useful for debugging.
+ --ask Ask to create directory if it desn't exist.
-h --help Show this help and exit
-m MG Path to the metagenomics paired files (must be 2 files).
-t MT Path to the metatranscriptomic paired files (2 files).
@@ -97,10 +98,9 @@ def run(args):
output = Path(args['-o']).abspath()
if not output.exists():
- if yes_or_no("Output '%s' doesn't exist. Create ?" % output):
- output.makedirs()
- else:
+ if args['--ask'] and not yes_or_no("Output '%s' doesn't exist. Create ?" % output):
exit(0)
+ output.makedirs()
container_name = args['-n'] is not None and args['-n'] or 'imp:latest'
db_path = Path(args['-d']).abspath()
# configure IMP mount point to the docker container
--
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