[med-svn] [Git][med-team/mindthegap][master] 2 commits: New upstream release version in changelog
Shayan Doust
gitlab at salsa.debian.org
Sun Jun 21 17:20:08 BST 2020
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 <hello at shayandoust.me>
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 <hello at shayandoust.me>
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 <hello at shayandoust.me>
-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
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