[med-svn] [salmon] 02/02: use Debian's libdivsufsort and libsparsehash
Sascha Steinbiss
satta at debian.org
Wed Sep 7 13:15:45 UTC 2016
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch master
in repository salmon.
commit 66054669d9d19f09541640db9ca3d93f541bbc9c
Author: Sascha Steinbiss <satta at debian.org>
Date: Wed Sep 7 13:15:30 2016 +0000
use Debian's libdivsufsort and libsparsehash
---
debian/control | 2 +
debian/patches/dependency-fix | 71 ++++++++++++++++++++++---
debian/patches/use_debian_packaged_rapmap.patch | 39 ++------------
3 files changed, 70 insertions(+), 42 deletions(-)
diff --git a/debian/control b/debian/control
index efc3742..de6d553 100644
--- a/debian/control
+++ b/debian/control
@@ -12,6 +12,8 @@ Build-Depends: debhelper (>= 9),
libboost-program-options-dev,
libboost-timer-dev,
libjellyfish-2.0-dev (>> 2.2.3-2),
+ libsparsehash-dev,
+ libdivsufsort-dev,
libbwa-dev,
pkg-config,
libjemalloc-dev,
diff --git a/debian/patches/dependency-fix b/debian/patches/dependency-fix
index 374ee9b..68a8c5d 100644
--- a/debian/patches/dependency-fix
+++ b/debian/patches/dependency-fix
@@ -29,10 +29,24 @@ Description: Use Debian version of dependencies, don't download them
message("BOOST_INCLUDEDIR = ${BOOST_INCLUDEDIR}")
message("BOOST_LIBRARYDIR = ${BOOST_LIBRARYDIR}")
message("Boost_FOUND = ${Boost_FOUND}")
-@@ -347,56 +347,56 @@
- )
- set(SUFFARRAY_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
+@@ -333,70 +333,70 @@
+ set(EXTERNAL_LIBRARY_PATH $CMAKE_CURRENT_SOURCE_DIR/lib)
+
+-message("Build system will build libdivsufsort")
+-message("==================================================================")
+-include(ExternalProject)
+-ExternalProject_Add(libdivsufsort
+- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+- URL ${CMAKE_CURRENT_SOURCE_DIR}/external/libdivsufsort.zip
+- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libdivsufsort-master
+- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+- UPDATE_COMMAND sh -c "mkdir -p <SOURCE_DIR>/build"
+- BINARY_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libdivsufsort-master/build
+- CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=<INSTALL_DIR> -DBUILD_DIVSUFSORT64=TRUE -DUSE_OPENMP=TRUE -DBUILD_SHARED_LIBS=FALSE
+-)
+-set(SUFFARRAY_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
+-
-message("Build system will fetch and build the Cereal serialization library")
-message("==================================================================")
-include(ExternalProject)
@@ -83,6 +97,20 @@ Description: Use Debian version of dependencies, don't download them
- INSTALL_COMMAND make install
-)
-endif()
++#message("Build system will build libdivsufsort")
++#message("==================================================================")
++#include(ExternalProject)
++#ExternalProject_Add(libdivsufsort
++# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
++# URL ${CMAKE_CURRENT_SOURCE_DIR}/external/libdivsufsort.zip
++# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libdivsufsort-master
++# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
++# UPDATE_COMMAND sh -c "mkdir -p <SOURCE_DIR>/build"
++# BINARY_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libdivsufsort-master/build
++# CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=<INSTALL_DIR> -DBUILD_DIVSUFSORT64=TRUE -DUSE_OPENMP=TRUE -DBUILD_SHARED_LIBS=FALSE
++#)
++#set(SUFFARRAY_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
++
+#message("Build system will fetch and build the Cereal serialization library")
+#message("==================================================================")
+#include(ExternalProject)
@@ -175,7 +203,8 @@ Description: Use Debian version of dependencies, don't download them
## GCC, get rid of the DO_ITT_NOTIFY flag
set(TBB_CXXFLAGS "${TBB_CXXFLAGS} -UDO_ITT_NOTIFY")
-endif()
--
++#endif()
+
-ExternalProject_Add(libtbb
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
- URL https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160526oss_src_0.tgz
@@ -189,8 +218,7 @@ Description: Use Debian version of dependencies, don't download them
- INSTALL_COMMAND sh -c "cp ${TBB_SOURCE_DIR}/build/LIBS_release/*.${SHARED_LIB_EXTENSION}* ${TBB_INSTALL_DIR}/lib && cp -r ${TBB_SOURCE_DIR}/include/* ${TBB_INSTALL_DIR}/include"
- BUILD_IN_SOURCE 1
-)
-+#endif()
-
+-
-SET( RECONFIG_FLAGS ${RECONFIG_FLAGS} -DTBB_WILL_RECONFIGURE=FALSE -DTBB_RECONFIGURE=TRUE)
-ExternalProject_Add_Step(libtbb reconfigure
- COMMAND ${CMAKE_COMMAND} ${CMAKE_CURRENT_SOURCE_DIR} ${RECONFIG_FLAGS}
@@ -370,7 +398,7 @@ Description: Use Debian version of dependencies, don't download them
set (FAST_MALLOC_LIB "")
set (HAVE_FAST_MALLOC FALSE)
-@@ -558,23 +558,23 @@
+@@ -558,40 +558,40 @@
endif()
endif()
@@ -411,6 +439,35 @@ Description: Use Debian version of dependencies, don't download them
##
+ ## This depenency is for RapMap
+ ##
+-message("Build system will fetch and build SparseHash")
+-message("==================================================================")
+-ExternalProject_Add(libsparsehash
+- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/sparsehash/archive/sparsehash-2.0.2.tar.gz -o sparsehash-2.0.2.tar.gz &&
+- tar -xzf sparsehash-2.0.2.tar.gz
+- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/sparsehash-sparsehash-2.0.2
+- BUILD_IN_SOURCE TRUE
+- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+- CONFIGURE_COMMAND sh -c "CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ./configure --prefix=<INSTALL_DIR>"
+- INSTALL_COMMAND make install
+-)
++#message("Build system will fetch and build SparseHash")
++#message("==================================================================")
++#ExternalProject_Add(libsparsehash
++# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
++# DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/sparsehash/archive/sparsehash-2.0.2.tar.gz -o sparsehash-2.0.2.tar.gz &&
++# tar -xzf sparsehash-2.0.2.tar.gz
++# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/sparsehash-sparsehash-2.0.2
++# BUILD_IN_SOURCE TRUE
++# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
++# CONFIGURE_COMMAND sh -c "CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ./configure --prefix=<INSTALL_DIR>"
++# INSTALL_COMMAND make install
++#)
+
+ ###
+ #
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1,11 +1,7 @@
diff --git a/debian/patches/use_debian_packaged_rapmap.patch b/debian/patches/use_debian_packaged_rapmap.patch
index 1fc2b2d..8c12145 100644
--- a/debian/patches/use_debian_packaged_rapmap.patch
+++ b/debian/patches/use_debian_packaged_rapmap.patch
@@ -1,6 +1,6 @@
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
-@@ -5,7 +5,6 @@ ${GAT_SOURCE_DIR}/include
+@@ -5,7 +5,6 @@
${ZLIB_INCLUDE_DIR}
${TBB_INCLUDE_DIRS}
${Boost_INCLUDE_DIRS}
@@ -8,7 +8,7 @@
)
if (JELLYFISH_FOUND)
-@@ -20,14 +19,6 @@ is.c
+@@ -20,14 +19,6 @@
bwt_gen.c
bwtindex.c
xxhash.c
@@ -23,7 +23,7 @@
CollapsedEMOptimizer.cpp
CollapsedGibbsSampler.cpp
Salmon.cpp
-@@ -39,7 +30,6 @@ SequenceBiasModel.cpp
+@@ -39,7 +30,6 @@
StadenUtils.cpp
TranscriptGroup.cpp
GZipWriter.cpp
@@ -33,7 +33,7 @@
set (SALMON_ALIGN_SRCS
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-@@ -161,7 +161,7 @@ set (CMAKE_VERBOSE_MAKEFILE true)
+@@ -161,7 +161,7 @@
#
####
if(NOT FETCHED_RAPMAP)
@@ -42,34 +42,3 @@
set(FETCHED_RAPMAP TRUE CACHE BOOL "Has RapMap been fetched?" FORCE)
endif()
-@@ -584,18 +584,18 @@ endif()
- ##
- ## This depenency is for RapMap
- ##
--message("Build system will fetch and build SparseHash")
--message("==================================================================")
--ExternalProject_Add(libsparsehash
-- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/sparsehash/archive/sparsehash-2.0.2.tar.gz -o sparsehash-2.0.2.tar.gz &&
-- tar -xzf sparsehash-2.0.2.tar.gz
-- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/sparsehash-sparsehash-2.0.2
-- BUILD_IN_SOURCE TRUE
-- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-- CONFIGURE_COMMAND sh -c "CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ./configure --prefix=<INSTALL_DIR>"
-- INSTALL_COMMAND make install
--)
-+#message("Build system will fetch and build SparseHash")
-+#message("==================================================================")
-+#ExternalProject_Add(libsparsehash
-+# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-+# DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/sparsehash/archive/sparsehash-2.0.2.tar.gz -o sparsehash-2.0.2.tar.gz &&
-+# tar -xzf sparsehash-2.0.2.tar.gz
-+# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/sparsehash-sparsehash-2.0.2
-+# BUILD_IN_SOURCE TRUE
-+# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-+# CONFIGURE_COMMAND sh -c "CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ./configure --prefix=<INSTALL_DIR>"
-+# INSTALL_COMMAND make install
-+#)
-
- ###
- #
--
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