Shayan Doust pushed to branch master at Debian Med / simka
Commits: b5adbf26 by Shayan Doust at 2019-09-08T23:29:50Z Add depends and build-depends - - - - - 6b51d26e by Shayan Doust at 2019-09-08T23:35:41Z Use debian packaged gatbcore instead of the one shipped as a module This currently causes problems in the program's linking stage (symbolic fails between src/* files) and needs looking at - - - - - 3 changed files: - debian/control - + debian/patches/series - + debian/patches/use_debian_packaged_libraries.patch Changes: ===================================== debian/control ===================================== @@ -3,7 +3,12 @@ Maintainer: Debian Med Packaging Team <[email protected]. Uploaders: Shayan Doust <[email protected]> Section: science Priority: optional -Build-Depends: debhelper-compat (= 12) +Build-Depends: debhelper-compat (= 12), + cmake, + libgatbcore-dev, + zlib1g-dev, + libhdf5-dev, + libboost-dev Standards-Version: 4.3.0 Vcs-Browser: https://salsa.debian.org/med-team/simka Vcs-Git: https://salsa.debian.org/med-team/simka.git @@ -12,7 +17,8 @@ Homepage: https://github.com/GATB/simka Package: simka Architecture: any Depends: ${shlibs:Depends}, - ${misc:Depends} + ${misc:Depends}, + libgatbcore2 Description: comparative metagenomics method dedicated to NGS datasets Simka is a de novo comparative metagenomics tool. Simka represents each dataset as a k-mer spectrum and compute several classical ecological ===================================== debian/patches/series ===================================== @@ -0,0 +1 @@ +use_debian_packaged_libraries.patch ===================================== debian/patches/use_debian_packaged_libraries.patch ===================================== @@ -0,0 +1,46 @@ +Description: use system-wide debian packaged libraries instead + This is instead of relying on cmake to compile and link against the libraries included within simka +Author: Shayan Doust <[email protected]> +Last-Update: 2019-09-09 +--- + +Index: simka/CMakeLists.txt +=================================================================== +--- simka.orig/CMakeLists.txt 2019-09-09 00:33:37.199917577 +0100 ++++ simka/CMakeLists.txt 2019-09-09 00:33:37.191917578 +0100 +@@ -42,7 +42,10 @@ + SET (GATB_CORE_EXCLUDE_EXAMPLES 1) + + # GATB CORE +-include (GatbCore) ++#include (GatbCore) ++ ++include(GNUInstallDirs) ++link_directories (/usr/${CMAKE_INSTALL_LIBDIR}/hdf5/serial) + + ################################################################################ + # TOOL +@@ -78,18 +81,18 @@ + set(PROJECT_BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR}/bin) + + add_executable (simka src/SimkaPotara.cpp ${ProjectFiles}) +-target_link_libraries (simka ${gatb-core-libraries}) ++target_link_libraries (simka ${gatb-core-libraries} gatbcore hdf5 z) + + add_executable (simkaCountProcess src/minikc/SimkaCountProcess.cpp ${ProjectFiles}) +-target_link_libraries (simkaCountProcess ${gatb-core-libraries}) ++target_link_libraries (simkaCountProcess ${gatb-core-libraries} gatbcore hdf5 z) + add_executable (simkaCount src/SimkaCount.cpp ${ProjectFiles}) +-target_link_libraries (simkaCount ${gatb-core-libraries}) ++target_link_libraries (simkaCount ${gatb-core-libraries} gatbcore hdf5 z) + + add_executable (simkaMerge src/SimkaMerge.cpp ${ProjectFiles}) +-target_link_libraries (simkaMerge ${gatb-core-libraries}) ++target_link_libraries (simkaMerge ${gatb-core-libraries} gatbcore hdf5 z) + + add_executable (simkaMinCore src/simkaMin/SimkaMin.cpp ${SimkaMinFiles}) +-target_link_libraries (simkaMinCore ${gatb-core-libraries}) ++target_link_libraries (simkaMinCore ${gatb-core-libraries} gatbcore hdf5 z) + + ################################################################################ + # PACKAGING View it on GitLab: https://salsa.debian.org/med-team/simka/compare/fef5006c2d6e4c3c224e187ecf2eb68a5f364cab...6b51d26e84ced0ffa9c23bd3a3bfa5296d2f33f3 -- View it on GitLab: https://salsa.debian.org/med-team/simka/compare/fef5006c2d6e4c3c224e187ecf2eb68a5f364cab...6b51d26e84ced0ffa9c23bd3a3bfa5296d2f33f3 You're receiving this email because of your account on salsa.debian.org.
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