[med-svn] [augustus] 01/01: update deps

[Sascha Steinbiss]

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

sascha-guest pushed a commit to branch master
in repository augustus.

commit f00bfb1d5338c8562c2399c8d263acfb6c33c7e2
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Sat Mar 19 21:44:42 2016 +0000

    update deps
---
 debian/control                |  6 +++---
 debian/patches/build_auxprogs | 15 +++++++++++++++
 debian/rules                  |  6 +++++-
 3 files changed, 23 insertions(+), 4 deletions(-)

diff --git a/debian/control b/debian/control
index f37a6e3..6c6e745 100644
--- a/debian/control
+++ b/debian/control
@@ -4,7 +4,7 @@ Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Sascha Steinbiss <sascha at steinbiss.name>
 Build-Depends: debhelper (>= 9), libsqlite3-dev, libboost-iostreams-dev,
-               zlib1g-dev, libgsl0-dev, libboost-graph-dev, liblpsolve55-dev,
+               zlib1g-dev, libgsl-dev, liblpsolve55-dev,
                libbamtools-dev, libbam-dev, libhts-dev, libncurses5-dev
 Standards-Version: 3.9.7
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/augustus.git
@@ -15,10 +15,10 @@ Package: augustus
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         libgsl0ldbl,
+         libgsl2,
          zlib1g,
          augustus-data,
-         libbamtools2.3.0,
+         libbamtools2.4.0,
          libhts1,
          libncurses5
 Suggests: augustus-auxprogs
diff --git a/debian/patches/build_auxprogs b/debian/patches/build_auxprogs
index b1a4f38..b572d98 100644
--- a/debian/patches/build_auxprogs
+++ b/debian/patches/build_auxprogs
@@ -199,3 +199,18 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
  
  clean:
  	rm -rf *o joingenes; rm -rf ../../bin/joingenes
+--- a/auxprogs/aln2wig/Makefile
++++ b/auxprogs/aln2wig/Makefile
+@@ -1,10 +1,10 @@
+ CFLAGS := -Wall -Wno-sign-compare -ansi -pedantic -O2 -ggdb ${CFLAGS}
+ 
+ psl2wig : aln2wig.o
+-	gcc $(CFLAGS) -o aln2wig aln2wig.o;
++	gcc $(CFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o aln2wig aln2wig.o;
+ 	cp aln2wig ../../bin
+ psl2wig.o : aln2wig.c
+-	gcc $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -c aln2wig.c
++	gcc $(CPPFLAGS) $(CXXFLAGS) $(CFLAGS) $(LDFLAGS) -c aln2wig.c
+ 
+ all : psl2wig
+ 
diff --git a/debian/rules b/debian/rules
index 1721307..9b20d76 100755
--- a/debian/rules
+++ b/debian/rules
@@ -11,6 +11,8 @@ override_dh_auto_clean:
 	cd $(CURDIR)
 	cd auxprogs/homGeneMapping/src && $(MAKE) clean
 	cd $(CURDIR)
+	cd auxprogs/aln2wig && $(MAKE) clean
+	cd $(CURDIR)
 	cd auxprogs/joingenes && $(MAKE) clean
 	cd $(CURDIR)
 	dh_auto_clean
@@ -19,6 +21,8 @@ override_dh_auto_build:
 	dh_auto_build
 	cd auxprogs/bam2hints && $(MAKE)
 	cd $(CURDIR)
+	cd auxprogs/aln2wig && $(MAKE)
+	cd $(CURDIR)
 	cd auxprogs/checkTargetSortedness && $(MAKE)
 	cd $(CURDIR)
 	cd auxprogs/homGeneMapping/src && $(MAKE)
@@ -28,7 +32,7 @@ override_dh_auto_build:
 
 override_dh_auto_install:
 	mkdir -p      debian/augustus/usr/bin
-	install bin/augustus     debian/augustus/usr/bin
+	install bin/*     debian/augustus/usr/bin
 	mkdir -p      debian/augustus/usr/share/augustus
 	cp -r scripts debian/augustus/usr/share/augustus
 	chmod +x      debian/augustus/usr/share/augustus/scripts/checkUTR

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