Package: spades / 3.13.1+dfsg-2

0103_use-debian-packaged-bwa.patch Patch series | download
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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)