[med-svn] r22660 - trunk/packages/srst2/trunk/debian/patches
Andreas Tille
tille at moszumanska.debian.org
Tue Aug 9 21:29:42 UTC 2016
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
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