[med-svn] r22660 - trunk/packages/srst2/trunk/debian/patches

[Andreas Tille]

Author: tille
Date: 2016-08-09 21:29:41 +0000 (Tue, 09 Aug 2016)
New Revision: 22660

Added:
   trunk/packages/srst2/trunk/debian/patches/debug_test.patch
Modified:
   trunk/packages/srst2/trunk/debian/patches/add_usr_bin_python_to_scripts.patch
   trunk/packages/srst2/trunk/debian/patches/series
Log:
New upstream version.  Unfortunately build time test calling bowtie2 fails


Modified: trunk/packages/srst2/trunk/debian/patches/add_usr_bin_python_to_scripts.patch
===================================================================
--- trunk/packages/srst2/trunk/debian/patches/add_usr_bin_python_to_scripts.patch	2016-08-08 07:04:21 UTC (rev 22659)
+++ trunk/packages/srst2/trunk/debian/patches/add_usr_bin_python_to_scripts.patch	2016-08-09 21:29:41 UTC (rev 22660)
@@ -2,13 +2,6 @@
 Last-Update: Tue, 31 May 2016 15:02:45 +0200
 Description: Add missing interpreter line
 
---- a/database_clustering/VFDB_cdhit_to_csv.py
-+++ b/database_clustering/VFDB_cdhit_to_csv.py
-@@ -1,3 +1,4 @@
-+#!/usr/bin/python
- '''
- Created on 19/06/2013
- @author: Harriet Dashnow, Kat Holt
 --- a/database_clustering/VFDBgenus.py
 +++ b/database_clustering/VFDBgenus.py
 @@ -1,3 +1,4 @@
@@ -30,3 +23,10 @@
 -	
 \ No newline at end of file
 +	
+--- a/database_clustering/VFDB_cdhit_to_csv.py
++++ b/database_clustering/VFDB_cdhit_to_csv.py
+@@ -1,3 +1,4 @@
++#!/usr/bin/python
+ '''
+ Created on 19/06/2013
+ @author: Harriet Dashnow, Kat Holt

Added: trunk/packages/srst2/trunk/debian/patches/debug_test.patch
===================================================================
--- trunk/packages/srst2/trunk/debian/patches/debug_test.patch	                        (rev 0)
+++ trunk/packages/srst2/trunk/debian/patches/debug_test.patch	2016-08-09 21:29:41 UTC (rev 22660)
@@ -0,0 +1,22 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 09 Aug 2016 23:27:52 +0200
+Description: bowtie2 definitely stumbles upon -foo argument  - but what else might be wrong?
+
+--- a/tests/test_srst2.py
++++ b/tests/test_srst2.py
+@@ -169,12 +169,14 @@ class TestRunBowtie(unittest.TestCase):
+ 			'/usr/bin/bowtie2',
+ 			'-U', 'fastq',
+ 			'-S', 'mapping_file.sam',
+-			'-foo',
+ 			'--very-sensitive-local',
+ 			'--no-unal',
+ 			'-a',
+ 			'-x', 'db_path'
+ 		]
++		fp=open('srst2_debug_test','w')
++		print >>fp, expected_bowtie2_command
++		fp.close()
+ 		run_mock.assert_called_once_with(expected_bowtie2_command)
+ 
+ 	@patch('srst2.logging')

Modified: trunk/packages/srst2/trunk/debian/patches/series
===================================================================
--- trunk/packages/srst2/trunk/debian/patches/series	2016-08-08 07:04:21 UTC (rev 22659)
+++ trunk/packages/srst2/trunk/debian/patches/series	2016-08-09 21:29:41 UTC (rev 22660)
@@ -1,2 +1,3 @@
 check_command_line_arguments.patch
 add_usr_bin_python_to_scripts.patch
+debug_test.patch