[med-svn] [Git][med-team/discosnp][master] Adjust use_debian_packaged_gatb-core.patch to not include GatbCore

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / discosnp


Commits:
19aa94b5 by Étienne Mollier at 2021-12-07T22:31:37+01:00
Adjust use_debian_packaged_gatb-core.patch to not include GatbCore

The corresponding GatbCore.cmake file provided in Debian will make
cmake look for embedded copies of gatb-core within discosnp source
code.  This embedded copy being excluded on purpose, cmake execution
will fail if this GatbCore.cmake file is included.  Actually, all the
settings are already properly set by discosnp CMakeLists.txt file
modified by the patch, and the headers package of gatb-core provides
all the elements needed by discosnp to get gatb-core support, so let's
just remove the `include (GatbCore)`

- - - - -


1 changed file:

- debian/patches/use_debian_packaged_gatb-core.patch


Changes:

=====================================
debian/patches/use_debian_packaged_gatb-core.patch
=====================================
@@ -2,9 +2,9 @@ Author: Andreas Tille <tille at 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
-@@ -32,8 +32,8 @@ ENDIF()
+--- discosnp.orig/CMakeLists.txt
++++ discosnp/CMakeLists.txt
+@@ -32,8 +32,8 @@
  ################################################################################
  # Define cmake modules directory
  ################################################################################
@@ -15,9 +15,19 @@ Description: Use cmake input file of Debian packaged gatb-core
  
  ################################################################################
  # THIRD PARTIES
---- a/tools/QHC/CMakeLists.txt
-+++ b/tools/QHC/CMakeLists.txt
-@@ -16,13 +16,15 @@ include_directories (src  ${gatb-core-in
+@@ -43,9 +43,6 @@
+ SET (GATB_CORE_EXCLUDE_TESTS     1)
+ SET (GATB_CORE_EXCLUDE_EXAMPLES  1)
+ 
+-# GATB CORE
+-include (GatbCore)
+-
+ ################################################################################
+ #  TOOLS GENERATION
+ ################################################################################
+--- discosnp.orig/tools/QHC/CMakeLists.txt
++++ discosnp/tools/QHC/CMakeLists.txt
+@@ -16,13 +16,15 @@
  file (GLOB_RECURSE  ProjectFiles  src/*)
  
  # we define the artifact to be built: the project binary
@@ -34,9 +44,9 @@ Description: Use cmake input file of Debian packaged gatb-core
  
  
  # We copy the project binary to the 'bin' directory
---- a/tools/kissnp2/CMakeLists.txt
-+++ b/tools/kissnp2/CMakeLists.txt
-@@ -16,14 +16,16 @@ include_directories (src  ${gatb-core-in
+--- discosnp.orig/tools/kissnp2/CMakeLists.txt
++++ discosnp/tools/kissnp2/CMakeLists.txt
+@@ -16,14 +16,16 @@
  file (GLOB_RECURSE  ProjectFiles  src/*)
  
  # we define the artifact to be built: the project binary
@@ -56,9 +66,9 @@ Description: Use cmake input file of Debian packaged gatb-core
 -INSTALL (TARGETS ${PROJECT_NAME} DESTINATION bin)
 \ No newline at end of file
 +INSTALL (TARGETS ${PROJECT_NAME} DESTINATION bin)
---- a/tools/kissreads2/CMakeLists.txt
-+++ b/tools/kissreads2/CMakeLists.txt
-@@ -16,14 +16,16 @@ include_directories (src  ${gatb-core-in
+--- discosnp.orig/tools/kissreads2/CMakeLists.txt
++++ discosnp/tools/kissreads2/CMakeLists.txt
+@@ -16,14 +16,16 @@
  file (GLOB_RECURSE  ProjectFiles  src/*)
  
  # we define the artifact to be built: the project binary
@@ -78,9 +88,9 @@ Description: Use cmake input file of Debian packaged gatb-core
 -INSTALL (TARGETS ${PROJECT_NAME} DESTINATION bin)
 \ No newline at end of file
 +INSTALL (TARGETS ${PROJECT_NAME} DESTINATION bin)
---- a/tools/read_file_names/CMakeLists.txt
-+++ b/tools/read_file_names/CMakeLists.txt
-@@ -16,14 +16,16 @@ include_directories (src  ${gatb-core-in
+--- discosnp.orig/tools/read_file_names/CMakeLists.txt
++++ discosnp/tools/read_file_names/CMakeLists.txt
+@@ -16,14 +16,16 @@
  file (GLOB_RECURSE  ProjectFiles  src/*)
  
  # we define the artifact to be built: the project binary
@@ -100,9 +110,9 @@ Description: Use cmake input file of Debian packaged gatb-core
 -INSTALL (TARGETS ${PROJECT_NAME} DESTINATION bin)
 \ No newline at end of file
 +INSTALL (TARGETS ${PROJECT_NAME} DESTINATION bin)
---- a/tools/create_coverage_h5_file/CMakeLists.txt
-+++ b/tools/create_coverage_h5_file/CMakeLists.txt
-@@ -16,14 +16,16 @@ include_directories (src  ${gatb-core-in
+--- discosnp.orig/tools/create_coverage_h5_file/CMakeLists.txt
++++ discosnp/tools/create_coverage_h5_file/CMakeLists.txt
+@@ -16,14 +16,16 @@
  file (GLOB_RECURSE  ProjectFiles  src/*)
  
  # we define the artifact to be built: the project binary



View it on GitLab: https://salsa.debian.org/med-team/discosnp/-/commit/19aa94b57c2b2c00797b66f26893ebc9e97cbd9b

-- 
View it on GitLab: https://salsa.debian.org/med-team/discosnp/-/commit/19aa94b57c2b2c00797b66f26893ebc9e97cbd9b
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