Shayan Doust pushed to branch master at Debian Med / mindthegap
Commits: 5c8c65e7 by Shayan Doust at 2020-06-21T17:02:06+01:00 New upstream release version in changelog - - - - - 8324e13c by Shayan Doust at 2020-06-21T17:19:53+01:00 Refresh patches - - - - - 4 changed files: - debian/changelog - debian/patches/modify_tests_for_autopkgtest.patch - debian/patches/remove_unnecessary_installs.patch - debian/patches/use_debian_packaged_gatb-core.patch Changes: ===================================== debian/changelog ===================================== @@ -1,4 +1,4 @@ -mindthegap (2.2.0-1) unstable; urgency=medium +mindthegap (2.2.2-1) unstable; urgency=medium * Initial release (Closes: #931826) ===================================== debian/patches/modify_tests_for_autopkgtest.patch ===================================== @@ -3,8 +3,6 @@ Description: Fix upstream pre-existing test scripts Author: Shayan Doust <[email protected]> Last-Update: 2019-07-09 -Index: mindthegap/test/simple_full_test.sh -=================================================================== --- mindthegap.orig/test/simple_full_test.sh +++ mindthegap/test/simple_full_test.sh @@ -1,18 +1,5 @@ @@ -26,7 +24,7 @@ Index: mindthegap/test/simple_full_test.sh RETVAL=0 testDir="test-output" outputPrefix=$testDir/full-test -@@ -33,7 +20,7 @@ mkdir $testDir +@@ -33,7 +20,7 @@ ################################################################################ # we launch the find module ################################################################################ @@ -35,7 +33,7 @@ Index: mindthegap/test/simple_full_test.sh ################################################################################ # we check the results -@@ -78,7 +65,7 @@ fi +@@ -121,7 +108,7 @@ ################################################################################ # we launch the fill module ################################################################################ @@ -44,7 +42,7 @@ Index: mindthegap/test/simple_full_test.sh ################################################################################ # we check the results -@@ -117,7 +104,7 @@ fi +@@ -160,7 +147,7 @@ ################################################################################ # we launch the fill module in contig mode ################################################################################ @@ -53,8 +51,6 @@ Index: mindthegap/test/simple_full_test.sh ################################################################################ # we check the results -Index: mindthegap/test/simple_test.sh -=================================================================== --- mindthegap.orig/test/simple_test.sh +++ mindthegap/test/simple_test.sh @@ -1,26 +1,13 @@ @@ -86,7 +82,7 @@ Index: mindthegap/test/simple_test.sh tmp1=output/$4_fill.insertions.fasta.tmp tmp2=output/tmp2 -@@ -45,7 +32,7 @@ run_test() +@@ -45,7 +32,7 @@ run_test_vcf() { # param : reads_file ref_file true_result prefix ===================================== debian/patches/remove_unnecessary_installs.patch ===================================== @@ -3,11 +3,9 @@ Description: Prevent CMake from installing some static files Author: Shayan Doust <[email protected]> Last-Update: 2019-07-09 -Index: mindthegap/CMakeLists.txt -=================================================================== --- mindthegap.orig/CMakeLists.txt +++ mindthegap/CMakeLists.txt -@@ -148,12 +148,12 @@ SET (CPACK_SOURCE_IGNORE_FILES +@@ -150,12 +150,12 @@ # We copy the project binary to the 'bin' directory INSTALL (TARGETS ${PROJECT_NAME} DESTINATION bin) ===================================== debian/patches/use_debian_packaged_gatb-core.patch ===================================== @@ -1,34 +1,55 @@ Description: Modify CMakeLists.txt ...to allow for CMake to use system-wide libraries instead of a localised binary within the same dir tree. Author: Shayan Doust <[email protected]> -Last-Update: 2019-07-09 - -Index: mindthegap/CMakeLists.txt -=================================================================== +Last-Update: 2020-06-21 --- mindthegap.orig/CMakeLists.txt +++ mindthegap/CMakeLists.txt -@@ -71,7 +71,7 @@ SET (GATB_CORE_EXCLUDE_TESTS 1) +@@ -51,7 +51,7 @@ + ################################################################################ + # Define cmake modules directory + ################################################################################ +-SET (GATB_CORE_HOME ${PROJECT_SOURCE_DIR}/thirdparty/gatb-core/gatb-core) ++#SET (GATB_CORE_HOME ${PROJECT_SOURCE_DIR}/thirdparty/gatb-core/gatb-core) + SET (CMAKE_MODULE_PATH ${GATB_CORE_HOME}/cmake) + + ################################################################################ +@@ -71,7 +71,7 @@ SET (GATB_CORE_EXCLUDE_EXAMPLES 1) # GATB CORE -include (GatbCore) -+# include (GatbCore) ++#include (GatbCore) ################################################################################ # TOOL -@@ -106,11 +106,14 @@ set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMA - # we define the files to be compiled - file (GLOB_RECURSE ProjectFiles src/*) +@@ -85,7 +85,8 @@ + + message("-- cxx: ${CMAKE_CXX_FLAGS}") + +- ++include (GNUInstallDirs) ++LINK_DIRECTORIES (/usr/${CMAKE_INSTALL_LIBDIR}/hdf5/serial) -+include(GNUInstallDirs) -+LINK_DIRECTORIES ( /usr/${CMAKE_INSTALL_LIBDIR}/hdf5/serial ) -+ - # we define the artifact to be built: the project binary - add_executable (${PROJECT_NAME} src/main.cpp ${ProjectFiles}) + # we get compilation definitions from the gatb-core part + add_definitions (${gatb-core-flags}) +@@ -99,7 +100,8 @@ + # - from dsk source + set (PROGRAM_SOURCE_DIR ${PROJECT_SOURCE_DIR}/src) + +-include_directories (${PROGRAM_SOURCE_DIR} ${gatb-core-includes}) ++#include_directories (${PROGRAM_SOURCE_DIR} ${gatb-core-includes}) ++include_directories (${PROGRAM_SOURCE_DIR} src/*) + + set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin) + +@@ -112,8 +114,8 @@ + add_executable(nwalign src/nwAlign/nwalign.cpp) # we define which libraries to be linked with project binary -target_link_libraries (${PROJECT_NAME} ${gatb-core-libraries}) -+target_link_libraries (${PROJECT_NAME} gatbcore hdf5) +-target_link_libraries (nwalign ${gatb-core-libraries}) ++target_link_libraries (${PROJECT_NAME} gatbcore hdf5) ++target_link_libraries (nwalign gatbcore hdf5) + - ################################################################################ View it on GitLab: https://salsa.debian.org/med-team/mindthegap/-/compare/8d91b0c78295095ab94121978e603c0730c9e40c...8324e13cb450cbb781802752871ff2eae32c5cff -- View it on GitLab: https://salsa.debian.org/med-team/mindthegap/-/compare/8d91b0c78295095ab94121978e603c0730c9e40c...8324e13cb450cbb781802752871ff2eae32c5cff You're receiving this email because of your account on salsa.debian.org.
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