debian/changelog

 skesa (2.3.0-1) UNRELEASED; urgency=medium
 
   * Initial release (Closes: #<bug>)
-  TODO: https://github.com/ncbi/ngs
 
  -- Andreas Tille <tille@debian.org>  Wed, 17 Jul 2019 10:54:03 +0200

debian/control

@@ -3,7 +3,16 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 12~)
+Build-Depends: debhelper (>= 12~),
+               libboost-dev,
+               libboost-chrono-dev,
+               libboost-iostreams-dev,
+               libboost-program-options-dev,
+               libboost-regex-dev,
+               libboost-system-dev,
+               libboost-timer-dev,
+               libncbi-vdb-dev,
+               libngs-sdk-dev
 Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/skesa
 Vcs-Git: https://salsa.debian.org/med-team/skesa.git

debian/patches/series

+use_debian_packaged_ngs-sdk.patch

debian/patches/use_debian_packaged_ngs-sdk.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Wed, 17 Jul 2019 10:54:03 +0200
+Description: Use Debian packaged ngs-sdk
+
+--- a/Makefile
++++ b/Makefile
+@@ -43,7 +43,7 @@ CC = c++ -std=c++11
+ CFLAGS = -Wall -Wno-format-y2k  -pthread -fPIC -O3 -finline-functions -fstrict-aliasing \
+          -fomit-frame-pointer -msse4.2 $(BOOST_INCL) $(NGS_INCL) $(VDB_INCL)
+          
+-LIBS = $(VDB_LIB) -lncbi-ngs-c++-static -lncbi-vdb-static \
++LIBS = $(VDB_LIB) -lncbi-ngs-c++ -lncbi-vdb \
+        $(NGS_LIB) -lngs-c++-static \
+        -Wl,-Bstatic $(BOOST_LIB) \
+        -lboost_program_options \
+@@ -61,7 +61,7 @@ all: skesa
+ 
+ glb_align.o: glb_align.hpp Makefile
+ 
+-skesa.o: common_util.hpp concurrenthash.hpp readsgetter.hpp ngs_includes.hpp counter.hpp graphdigger.hpp assembler.hpp KmerInit.hpp DBGraph.hpp Integer.hpp LargeInt.hpp LargeInt1.hpp LargeInt2.hpp Model.hpp config.hpp Makefile $(NGS_DIR)/ngs.done
++skesa.o: common_util.hpp concurrenthash.hpp readsgetter.hpp ngs_includes.hpp counter.hpp graphdigger.hpp assembler.hpp KmerInit.hpp DBGraph.hpp Integer.hpp LargeInt.hpp LargeInt1.hpp LargeInt2.hpp Model.hpp config.hpp Makefile
+ skesa: skesa.o glb_align.o
+ 	$(CC) -o $@ $^ $(LIBS)
+ 
+--- a/ngs_includes.hpp
++++ b/ngs_includes.hpp
+@@ -24,7 +24,7 @@
+ *
+ */
+ 
+-#include <ncbi-vdb/NGS.hpp>
++#include <ncbi-vdb/ngs/ncbi/NGS.hpp>
+ #include <ngs/ErrorMsg.hpp>
+ #include <ngs/ReadCollection.hpp>
+ #include <ngs/ReadIterator.hpp>