1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
|
Author: Andreas Tille <tille@debian.org>
Last-Changed: Tue, 18 Feb 2014 15:48:55 +0100
Description: SPAdes originally contained a code copy of bwa since the version
of bwa which was current of the time of release did not builded with recent
gcc versions. Since this is not the case with Debian shipped bwa this code
copy is skipped.
.
See https://lists.debian.org/debian-med/2014/02/msg00192.html
.
Note: I tried to patch the Python scripts which were calling bwa-spades to
rather call /usr/bin/bwa but the test suite failed. So as an alternative
the package contains a symlink
ln -s /usr/bin/bwa /usr/lib/spades/bin/bwa-spades
which enables successful run of the test suite
--- a/assembler/ext/tools/CMakeLists.txt
+++ b/assembler/ext/tools/CMakeLists.txt
@@ -5,4 +5,3 @@
# See file LICENSE for details.
############################################################################
-add_subdirectory(bwa-0.7.12)
--- a/assembler/ext/src/CMakeLists.txt
+++ b/assembler/ext/src/CMakeLists.txt
@@ -11,7 +11,6 @@ add_subdirectory(cityhash)
add_subdirectory(getopt_pp)
add_subdirectory(llvm)
add_subdirectory(htrie)
-add_subdirectory(bwa)
add_subdirectory(gqf)
add_subdirectory(edlib)
add_subdirectory(gfa1)
|
