debian/changelog

@@ -10,7 +10,8 @@ minia (3.2.0-1) UNRELEASED; urgency=medium
   * Remove trailing whitespace in debian/changelog
   * Remove trailing whitespace in debian/control
   * Remove trailing whitespace in debian/copyright
-  * Build-Depends: libboost-dev, libgatbcore-dev
+  * Build-Depends: libboost-dev, libhdf5-dev
+  * Versioned Build-Depends: libgatbcore-dev (>= 1.4.1+git20181225.44d5a44~)
 
  -- Andreas Tille <tille@debian.org>  Mon, 21 Jan 2019 09:01:19 +0100
 

debian/control

@@ -9,7 +9,8 @@ Build-Depends: debhelper (>= 12~),
                bc,
                zlib1g-dev,
                libboost-dev,
-               libgatbcore-dev
+               libgatbcore-dev (>= 1.4.1+git20181225.44d5a44~),
+               libhdf5-dev
 Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/minia
 Vcs-Git: https://salsa.debian.org/med-team/minia.git

debian/docs

 debian/README.test
 debian/tests/run-unit-test
-test/read50x_ref10K_e001.fasta
+test/read50x_ref10K_e001.fa*
 

debian/minia.install

-minia usr/bin/

debian/patches/link_libraries.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Mon, 21 Jan 2019 09:01:19 +0100
+Description: Link against Debian packaged gatbcore
+
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -72,15 +72,17 @@ set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMA
+ 
+ include_directories (${PROGRAM_SOURCE_DIR})
+ file (GLOB_RECURSE  ProjectFiles  ${PROGRAM_SOURCE_DIR}/*)
++include(GNUInstallDirs)
++LINK_DIRECTORIES( /usr/${CMAKE_INSTALL_LIBDIR}/hdf5/serial )
+ add_executable(${PROJECT_NAME} ${ProjectFiles})
+-target_link_libraries(${PROJECT_NAME} ${gatb-core-libraries})
++target_link_libraries(${PROJECT_NAME} gatbcore hdf5 )
+ 
+ # merci
+ set (MERCI_SOURCE_DIR ${PROJECT_SOURCE_DIR}/merci)
+ include_directories (${MERCI_SOURCE_DIR})
+ file (GLOB_RECURSE  MerciFiles  ${MERCI_SOURCE_DIR}/*.cpp)
+ add_executable("merci"  ${MerciFiles})
+-target_link_libraries("merci" ${gatb-core-libraries})
++target_link_libraries("merci" gatbcore hdf5 )
+ 
+ 
+ ################################################################################

debian/patches/series

 use_debian_packaged_gatb-core.patch
+link_libraries.patch

debian/patches/use_debian_packaged_gatb-core.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Mon, 21 Jan 2019 09:01:19 +0100
+Description: Use cmake input file of Debian packaged gatb-core
+
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
-@@ -42,8 +42,8 @@ add_definitions( -DGIT_SHA1="${VERSION_S
+@@ -28,22 +28,11 @@ IF (DEFINED JENKINS_TAG)
+     SET (gatb-tool-version ${JENKINS_TAG})
+ ENDIF()
+ 
+-#############################
+-# getting git version
+-#from http://stackoverflow.com/questions/1435953/how-can-i-pass-git-sha1-to-compiler-as-definition-using-cmake
+-exec_program(
+-    "git"
+-    ${CMAKE_CURRENT_SOURCE_DIR}
+-    ARGS "rev-parse --short HEAD"
+-    OUTPUT_VARIABLE VERSION_SHA1 )
+-
+-add_definitions( -DGIT_SHA1="${VERSION_SHA1}" )
+-
  ################################################################################
  # Define cmake modules directory
  ################################################################################