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debian/control
View file @ 46844d11
......@@ -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
View file @ 46844d11
......@@ -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
View file @ 46844d11
......@@ -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)