[med-svn] [Git][med-team/sailfish][master] 2 commits: Build-Depends certain boost modules completed
Andreas Tille
gitlab at salsa.debian.org
Wed Mar 27 10:53:38 GMT 2019
Andreas Tille pushed to branch master at Debian Med / sailfish
Commits:
8ebfc862 by Andreas Tille at 2019-03-27T10:53:20Z
Build-Depends certain boost modules completed
- - - - -
46844d11 by Andreas Tille at 2019-03-27T10:53:20Z
Simplify patching by introducing DEBIAN_BUILD definition, keep on with cmake file patching
- - - - -
3 changed files:
- debian/control
- debian/patches/dfsg-please.patch
- debian/rules
Changes:
=====================================
debian/control
=====================================
@@ -6,7 +6,14 @@ Priority: optional
Build-Depends: debhelper (>= 12),
cmake,
zlib1g-dev,
- libboost-dev,
+ libboost-atomic-dev,
+ libboost-chrono-dev,
+ libboost-date-time-dev,
+ libboost-filesystem-dev,
+ libboost-iostreams-dev,
+ libboost-program-options-dev,
+ libboost-thread-dev,
+ libboost-timer-dev,
libtbb-dev,
libgff-dev,
libjellyfish-2.0-dev,
=====================================
debian/patches/dfsg-please.patch
=====================================
@@ -2,94 +2,73 @@ Author: Steffen Möller
Last-Update: 2019-03-25 23:34:53 +0100
Description: Make sure we build against Debian packaged libraries
-Index: sailfish-0.10.1/CMakeLists.txt
-===================================================================
---- sailfish-0.10.1.orig/CMakeLists.txt
-+++ sailfish-0.10.1/CMakeLists.txt
-@@ -287,22 +287,22 @@ ExternalProject_Add(libdivsufsort
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -287,6 +287,7 @@ ExternalProject_Add(libdivsufsort
set(SUFFARRAY_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
--message("Build system will fetch and build Jellyfish")
--message("==================================================================")
--ExternalProject_Add(libjellyfish
-- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L https://github.com/gmarcais/Jellyfish/releases/download/v2.2.3/jellyfish-2.2.3.tar.gz -o jellyfish-2.2.3.tgz &&
-- rm -fr jellyfish-2.2.3 &&
-- tar -xzvf jellyfish-2.2.3.tgz
-- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.3
-- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-- CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.3/configure --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${JELLYFISH_CXX_FLAGS}
-- BUILD_COMMAND ${MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${JELLYFISH_CXX_FLAGS}
-- BUILD_IN_SOURCE 1
-- INSTALL_COMMAND make install &&
-- cp config.h <INSTALL_DIR>/include/jellyfish-2.2.3/jellyfish/ &&
-- cp config.h <INSTALL_DIR>/include/
--)
-+#message("Build system will fetch and build Jellyfish")
-+#message("==================================================================")
-+#ExternalProject_Add(libjellyfish
-+# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-+# DOWNLOAD_COMMAND curl -k -L https://github.com/gmarcais/Jellyfish/releases/download/v2.2.3/jellyfish-2.2.3.tar.gz -o jellyfish-2.2.3.tgz &&
-+# rm -fr jellyfish-2.2.3 &&
-+# tar -xzvf jellyfish-2.2.3.tgz
-+# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.3
-+# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-+# CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.3/configure --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${JELLYFISH_CXX_FLAGS}
-+# BUILD_COMMAND ${MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${JELLYFISH_CXX_FLAGS}
-+# BUILD_IN_SOURCE 1
-+# INSTALL_COMMAND make install &&
-+# cp config.h <INSTALL_DIR>/include/jellyfish-2.2.3/jellyfish/ &&
-+# cp config.h <INSTALL_DIR>/include/
-+#)
++if(!DEBIAN_BUILD)
+ message("Build system will fetch and build Jellyfish")
+ message("==================================================================")
+ ExternalProject_Add(libjellyfish
+@@ -303,6 +304,9 @@ ExternalProject_Add(libjellyfish
+ cp config.h <INSTALL_DIR>/include/jellyfish-2.2.3/jellyfish/ &&
+ cp config.h <INSTALL_DIR>/include/
+ )
++else()
++message("Use Debian packaged Jellyfish")
++endif()
find_package(TBB)
##
-@@ -311,6 +311,9 @@ find_package(TBB)
+@@ -311,6 +315,7 @@ find_package(TBB)
#
##
if(NOT TBB_FOUND)
-+message("TBB not found: Build system would like to fetch and build Intel Threading Building Blocks")
-+
-+if(FALSE)
++if(!DEBIAN_BUILD)
set(TBB_WILL_RECONFIGURE TRUE)
# Set the appropriate compiler
-@@ -352,6 +355,7 @@ ExternalProject_Add_Step(libtbb reconfig
+@@ -352,6 +357,9 @@ ExternalProject_Add_Step(libtbb reconfig
DEPENDEES install
)
endif()
++else()
++ message("Use Debian packaged TBB")
+endif()
##
# Find HDF5, and prefer the static libs
-@@ -401,7 +405,7 @@ endif()
+@@ -401,7 +409,7 @@ endif()
message("TBB_LIBRARIES = ${TBB_LIBRARIES}")
-
-+if(FALSE)
++if(!DEBIAN_BUILD)
message("Build system will compile libgff")
message("==================================================================")
ExternalProject_Add(libgff
-@@ -416,6 +420,7 @@ ExternalProject_Add(libgff
+@@ -416,6 +424,9 @@ ExternalProject_Add(libgff
BINARY_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libgff/build
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_CURRENT_SOURCE_DIR}/external/install
)
++else()
++message("Use Debian packaged libgff")
+endif()
set (FAST_MALLOC_LIB "")
set (HAVE_FAST_MALLOC FALSE)
-@@ -441,6 +446,8 @@ endif()
+@@ -441,6 +452,8 @@ endif()
if (NOT HAVE_FAST_MALLOC)
message("Build system will fetch and use JEMalloc")
-+if(FALSE)
++if(!DEBIAN_BUILD)
+ message("Build system will fetch and use JEMalloc")
message("==================================================================")
ExternalProject_Add(libjemalloc
DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-@@ -456,10 +463,12 @@ if (NOT HAVE_FAST_MALLOC)
+@@ -456,10 +469,12 @@ if (NOT HAVE_FAST_MALLOC)
set (FAST_MALLOC_LIB ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib/libjemalloc.a)
set (HAVE_FAST_MALLOC TRUE)
endif ()
@@ -98,11 +77,11 @@ Index: sailfish-0.10.1/CMakeLists.txt
##
## This depenency is for RapMap
##
-+if(FALSE)
++if(!DEBIAN_BUILD)
message("Build system will fetch and build SparseHash")
message("==================================================================")
ExternalProject_Add(libsparsehash
-@@ -472,6 +481,7 @@ ExternalProject_Add(libsparsehash
+@@ -472,6 +487,7 @@ ExternalProject_Add(libsparsehash
CONFIGURE_COMMAND sh -c "CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ./configure --prefix=<INSTALL_DIR>"
INSTALL_COMMAND make install
)
@@ -110,10 +89,8 @@ Index: sailfish-0.10.1/CMakeLists.txt
###
#
-Index: sailfish-0.10.1/scripts/compile.sh
-===================================================================
---- sailfish-0.10.1.orig/scripts/compile.sh
-+++ sailfish-0.10.1/scripts/compile.sh
+--- a/scripts/compile.sh
++++ b/scripts/compile.sh
@@ -6,6 +6,8 @@ version=$2
echo "Building sailfish [branch = ${branch}]. Tagging version as ${version}"
@@ -123,3 +100,38 @@ Index: sailfish-0.10.1/scripts/compile.sh
# Activate Holy Build Box environment.
source /hbb_exe/activate
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -24,23 +24,23 @@ EmpiricalDistribution.cpp
+ #HDF5Writer.cpp
+ GZipWriter.cpp
+ xxhash.c
+-${GAT_SOURCE_DIR}/external/install/src/rapmap/RapMapFileSystem.cpp
+-${GAT_SOURCE_DIR}/external/install/src/rapmap/RapMapSAIndexer.cpp
+-${GAT_SOURCE_DIR}/external/install/src/rapmap/RapMapSAIndex.cpp
++#${GAT_SOURCE_DIR}/external/install/src/rapmap/RapMapFileSystem.cpp
++#${GAT_SOURCE_DIR}/external/install/src/rapmap/RapMapSAIndexer.cpp
++#${GAT_SOURCE_DIR}/external/install/src/rapmap/RapMapSAIndex.cpp
+ #${GAT_SOURCE_DIR}/external/install/src/rapmap/RapMapSAMapper.cpp
+-${GAT_SOURCE_DIR}/external/install/src/rapmap/RapMapUtils.cpp
+-${GAT_SOURCE_DIR}/external/install/src/rapmap/HitManager.cpp
+-${GAT_SOURCE_DIR}/external/install/src/rapmap/rank9b.cpp
+-${GAT_SOURCE_DIR}/external/install/src/rapmap/bit_array.c
++#${GAT_SOURCE_DIR}/external/install/src/rapmap/RapMapUtils.cpp
++#${GAT_SOURCE_DIR}/external/install/src/rapmap/HitManager.cpp
++#${GAT_SOURCE_DIR}/external/install/src/rapmap/rank9b.cpp
++#${GAT_SOURCE_DIR}/external/install/src/rapmap/bit_array.c
+ #${GAT_SOURCE_DIR}/external/install/src/EasyH5Utils.cpp
+ )
+
+ include_directories(
+ ${GAT_SOURCE_DIR}/tests
+ ${GAT_SOURCE_DIR}/include
+-${GAT_SOURCE_DIR}/include/eigen3
++/usr/include/eigen3
+ ${GAT_SOURCE_DIR}/external
+-${GAT_SOURCE_DIR}/external/cereal/include
++/usr/include/cereal
+ ${GAT_SOURCE_DIR}/external/install/include
+ ${GAT_SOURCE_DIR}/external/install/include/rapmap
+ ${GAT_SOURCE_DIR}/external/install/include/jellyfish-2.2.3
=====================================
debian/rules
=====================================
@@ -11,8 +11,10 @@
# package maintainers to append CFLAGS
#export DEB_CFLAGS_MAINT_APPEND = -Wall -pedantic
# package maintainers to append LDFLAGS
-#export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
+CMAKE_EXTRA_FLAGS += -DDEBIAN_BUILD=1 \
+ -DFETCHED_RAPMAP=1 \
+ -DCMAKE_FETCH_BOOST=FALSE
%:
dh $@
@@ -21,5 +23,4 @@
# dh_make generated override targets
# This is example for Cmake (See https://bugs.debian.org/641051 )
override_dh_auto_configure:
- dh_auto_configure -- -DCMAKE_FETCH_BOOST=FALSE # -DCMAKE_LIBRARY_PATH=$(DEB_HOST_MULTIARCH)
-
+ dh_auto_configure -- $(CMAKE_EXTRA_FLAGS) # -DCMAKE_LIBRARY_PATH=$(DEB_HOST_MULTIARCH)
View it on GitLab: https://salsa.debian.org/med-team/sailfish/compare/345ab5a23245fec14d5d17989edbb0105f530f2f...46844d11123591f90fa2362ea031fb6100450f79
--
View it on GitLab: https://salsa.debian.org/med-team/sailfish/compare/345ab5a23245fec14d5d17989edbb0105f530f2f...46844d11123591f90fa2362ea031fb6100450f79
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