Andreas Tille pushed to branch master at Debian Med / skesa
Commits: f58eaeea by Andreas Tille at 2019-07-17T09:47:12Z Fix Build-Depends - - - - - a0570959 by Andreas Tille at 2019-07-17T09:49:18Z Use Debian packaged ngs-sdk - - - - - 4 changed files: - debian/changelog - debian/control - + debian/patches/series - + debian/patches/use_debian_packaged_ngs-sdk.patch Changes: ===================================== debian/changelog ===================================== @@ -1,6 +1,5 @@ skesa (2.3.0-1) UNRELEASED; urgency=medium * Initial release (Closes: #<bug>) - TODO: https://github.com/ncbi/ngs -- Andreas Tille <[email protected]> Wed, 17 Jul 2019 10:54:03 +0200 ===================================== debian/control ===================================== @@ -3,7 +3,16 @@ Maintainer: Debian Med Packaging Team <[email protected]. Uploaders: Andreas Tille <[email protected]> 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 ===================================== @@ -0,0 +1 @@ +use_debian_packaged_ngs-sdk.patch ===================================== debian/patches/use_debian_packaged_ngs-sdk.patch ===================================== @@ -0,0 +1,35 @@ +Author: Andreas Tille <[email protected]> +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> View it on GitLab: https://salsa.debian.org/med-team/skesa/compare/19a1529697105741d88784fe781fc56b5d769dc1...a05709591305f031976222d390c17fe878dadede -- View it on GitLab: https://salsa.debian.org/med-team/skesa/compare/19a1529697105741d88784fe781fc56b5d769dc1...a05709591305f031976222d390c17fe878dadede You're receiving this email because of your account on salsa.debian.org.
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