[med-svn] [Git][med-team/sra-sdk][master] Find ncbi-vdb interfaces

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / sra-sdk


Commits:
f9185616 by Andreas Tille at 2022-07-27T15:58:12+02:00
Find ncbi-vdb interfaces

- - - - -


3 changed files:

- debian/control
- + debian/patches/find_ncbi-vdb-interfaces.patch
- debian/patches/series


Changes:

=====================================
debian/control
=====================================
@@ -8,7 +8,7 @@ Priority: optional
 Build-Depends: debhelper-compat (= 13),
                cmake,
                libngs-sdk-dev (>= 2.11.2),
-               libncbi-vdb-dev (>= 2.10.6+dfsg-3~),
+               libncbi-vdb-dev (>= 3.0.0+dfsg~),
                libvdb-sqlite-dev,
                libfuse-dev,
                libhdf5-dev,


=====================================
debian/patches/find_ncbi-vdb-interfaces.patch
=====================================
@@ -0,0 +1,36 @@
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -41,8 +41,8 @@ set(CMAKE_MODULE_PATH
+     "${CMAKE_CURRENT_SOURCE_DIR}/build"
+ )
+ 
+-set( VDB_BINDIR "${CMAKE_BINARY_DIR}/../ncbi-vdb" CACHE PATH "Location of NCBI VDB build directory" )
+-set( VDB_INCDIR "${CMAKE_SOURCE_DIR}/../ncbi-vdb/interfaces" CACHE PATH "Location of NCBI VDB include directory" )
++set( VDB_BINDIR "/usr/include/ncbi-vdb" CACHE PATH "Location of NCBI VDB build directory" )
++set( VDB_INCDIR "/usr/include/ncbi-vdb/interfaces" CACHE PATH "Location of NCBI VDB include directory" )
+ 
+ include( build/env.cmake NO_POLICY_SCOPE )
+ 
+--- a/tools/bam-loader/CMakeLists.txt
++++ b/tools/bam-loader/CMakeLists.txt
+@@ -24,7 +24,7 @@
+ 
+ add_compile_definitions( __mod__="tools/bam-loader" )
+ 
+-include_directories( ${CMAKE_SOURCE_DIR}/../ncbi-vdb/interfaces/ext/ ) # zlib.h
++include_directories( /usr/include/ncbi-vdb/interfaces/ext/ ) # zlib.h
+ 
+ # Internal
+ add_executable( samview
+--- a/tools2/shared/cmake/Findncbi-vdb.cmake
++++ b/tools2/shared/cmake/Findncbi-vdb.cmake
+@@ -44,7 +44,8 @@ elseif (NOT ncbi-vdb_FIND_QUIETLY)
+ endif ()
+ 
+ find_path (ncbi-vdb_INCLUDE_DIR "vdb/manager.h"
+-    PATHS   "../ncbi-vdb/interfaces"
++    PATHS   "/usr/include/ncbi-vdb/interfaces"
++            "../ncbi-vdb/interfaces"
+             "../../ncbi-vdb/interfaces"
+             "../../../ncbi-vdb/interfaces"
+             "../../../../ncbi-vdb/interfaces"


=====================================
debian/patches/series
=====================================
@@ -24,3 +24,4 @@ python3
 skip_test_using_lots_of_memory.patch
 allow_multi_help.patch
 run_unversioned_tools.patch
+find_ncbi-vdb-interfaces.patch



View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/commit/f9185616bef4e6144ae7d7e566cf3ddd7c750618

-- 
View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/commit/f9185616bef4e6144ae7d7e566cf3ddd7c750618
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