[med-svn] [Git][med-team/sra-sdk][master] Use Debian packaged re2 ... this does not work yet

[Andreas Tille (@tille)]

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


Commits:
da65c1ce by Andreas Tille at 2022-07-28T11:28:33+02:00
Use Debian packaged re2 ... this does not work yet

- - - - -


3 changed files:

- debian/control
- debian/patches/series
- + debian/patches/use_debian_packaged_re2.patch


Changes:

=====================================
debian/control
=====================================
@@ -13,6 +13,7 @@ Build-Depends: debhelper-compat (= 13),
                libfuse-dev,
                libhdf5-dev,
                libmagic-dev,
+               libre2-dev,
                libxml2-dev,
                libzstd-dev,
                python3,


=====================================
debian/patches/series
=====================================
@@ -25,3 +25,4 @@ skip_test_using_lots_of_memory.patch
 allow_multi_help.patch
 run_unversioned_tools.patch
 find_ncbi-vdb-interfaces.patch
+use_debian_packaged_re2.patch


=====================================
debian/patches/use_debian_packaged_re2.patch
=====================================
@@ -0,0 +1,67 @@
+--- a/tools/sharq/CMakeLists.txt
++++ b/tools/sharq/CMakeLists.txt
+@@ -58,27 +58,27 @@ set(LOCAL_INCDIR ${LOCAL_BUILD_DIR}/incl
+ set(LOCAL_LIBDIR ${LOCAL_BUILD_DIR}/lib)
+ 
+ # Google RE2 release
+-set(RE2_TAG 2021-09-01)
+-
+-include (ExternalProject)
+-ExternalProject_Add(RE2
+-  PREFIX RE2
+-  GIT_REPOSITORY https://github.com/google/re2.git
+-  GIT_TAG ${RE2_TAG}
+-  BUILD_IN_SOURCE 1
+-  UPDATE_COMMAND "" # No update as we use specific tag
+-  #INSTALL_DIR ${LOCAL_BUILD_DIR}
+-  CMAKE_ARGS
+-    -DCMAKE_BUILD_TYPE:STRING=Release
+-    -DRE2_BUILD_TESTING:BOOL=OFF
+-    -DCMAKE_INSTALL_PREFIX:PATH=${LOCAL_BUILD_DIR}
+-    -DCMAKE_INSTALL_LIBDIR:PATH=lib
+-    -DCMAKE_VERBOSE_MAKEFILE:BOOL=OFF
+-    -DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON
+-    -DCMAKE_INSTALL_MESSAGE:STRING=LAZY
+-
+-)
+-set(RE2_STATIC_LIBRARIES -L${LOCAL_LIBDIR} -lre2 )
++#set(RE2_TAG 2021-09-01)
++#
++#include (ExternalProject)
++#ExternalProject_Add(RE2
++#  PREFIX RE2
++#  GIT_REPOSITORY https://github.com/google/re2.git
++#  GIT_TAG ${RE2_TAG}
++#  BUILD_IN_SOURCE 1
++#  UPDATE_COMMAND "" # No update as we use specific tag
++#  #INSTALL_DIR ${LOCAL_BUILD_DIR}
++#  CMAKE_ARGS
++#    -DCMAKE_BUILD_TYPE:STRING=Release
++#    -DRE2_BUILD_TESTING:BOOL=OFF
++#    -DCMAKE_INSTALL_PREFIX:PATH=${LOCAL_BUILD_DIR}
++#    -DCMAKE_INSTALL_LIBDIR:PATH=lib
++#    -DCMAKE_VERBOSE_MAKEFILE:BOOL=OFF
++#    -DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON
++#    -DCMAKE_INSTALL_MESSAGE:STRING=LAZY
++#
++#)
++set(RE2_STATIC_LIBRARIES -lre2 )
+ 
+ #file(COPY ${CMAKE_SOURCE_DIR}/tools/sharq/sharq.py  DESTINATION ${BINDIR})
+ 
+@@ -90,7 +90,7 @@ add_custom_target(
+     ${BINDIR}/sharq.py)
+ 
+ add_executable(sharq fastq_parse)
+-add_dependencies(sharq RE2 sharq.py)
++add_dependencies(sharq sharq.py)
+ target_include_directories(sharq PUBLIC ${LOCAL_INCDIR} ./ ../../)
+ if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
+         set(CXX_FILESYSTEM_LIBRARIES "stdc++fs")
+@@ -100,4 +100,4 @@ MakeLinksExe( sharq false )
+ 
+ endif()
+ 
+-endif()
+\ No newline at end of file
++endif()



View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/commit/da65c1cec5f3e8ccb26cbc57d1c4b8e3b33d7647

-- 
View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/commit/da65c1cec5f3e8ccb26cbc57d1c4b8e3b33d7647
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