[med-svn] [freebayes] 01/01: Fix patch to install bamleftalign

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository freebayes.

commit 1256a5c43dc62a2ad4e197529ed2a8ab2351e674
Author: Andreas Tille <tille at debian.org>
Date:   Fri Jan 13 17:42:49 2017 +0100

    Fix patch to install bamleftalign
---
 debian/patches/use_debian_packaged_bamtools.patch | 2 +-
 debian/rules                                      | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/debian/patches/use_debian_packaged_bamtools.patch b/debian/patches/use_debian_packaged_bamtools.patch
index a420cf1..23f035e 100644
--- a/debian/patches/use_debian_packaged_bamtools.patch
+++ b/debian/patches/use_debian_packaged_bamtools.patch
@@ -46,7 +46,7 @@ Description: Use Debian packaged bamtools
 -bamleftalign ../bin/bamleftalign: $(BAMTOOLS_ROOT)/lib/libbamtools.a bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o
 -	$(CXX) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o $(BAMTOOLS_ROOT)/lib/libbamtools.a -o ../bin/bamleftalign $(LIBS)
 +bamleftalign ../bin/bamleftalign: bamleftalign.o Fasta.o
-+	$(CXX) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o -lbamtools
++	$(CXX) $(CFLAGS) $(INCLUDE) bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o -o ../bin/bamleftalign -lbamtools
  
 -bamfiltertech ../bin/bamfiltertech: $(BAMTOOLS_ROOT)/lib/libbamtools.a bamfiltertech.o $(OBJECTS) $(HEADERS)
 +bamfiltertech ../bin/bamfiltertech: bamfiltertech.o $(OBJECTS) $(HEADERS)
diff --git a/debian/rules b/debian/rules
index 6524b20..d0ad0c5 100755
--- a/debian/rules
+++ b/debian/rules
@@ -9,5 +9,5 @@ override_dh_auto_install:
 override_dh_auto_test:
 	mkdir -p $(CURDIR)/test/bash-tap/
 	for bt in $(CURDIR)/debian/bash-tap/* ; do ln -s $${bt} $(CURDIR)/test/bash-tap/`basename $${bt}` ; done
-	dh_auto_test
+	export PATH=/usr/lib/vcflib/binaries/:$(PATH) dh_auto_test
 	rm -rf $(CURDIR)/test/bash-tap

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/freebayes.git