debian/control

@@ -3,7 +3,12 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Shayan Doust <hello@shayandoust.me>
 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

+use_debian_packaged_libraries.patch

debian/patches/use_debian_packaged_libraries.patch

+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 <hello@shayandoust.me>
+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