[med-svn] [salmon] 04/09: Try to adapt patches to new upstream version. PLEASE VERIFY!!!
Andreas Tille
tille at debian.org
Tue Aug 30 10:12:30 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository salmon.
commit 0954b5d21b1198d6366981939ad35d9212291fdd
Author: Andreas Tille <tille at debian.org>
Date: Tue Aug 30 11:54:03 2016 +0200
Try to adapt patches to new upstream version. PLEASE VERIFY!!!
---
CMakeLists.txt | 348 +++++++++++----------
...007-Remove-unnecessarily-linked-libraries.patch | 34 +-
debian/patches/0008-Remove-salmon_core-lib.patch | 22 +-
...emove-FIND_PACKAGE-for-liblzma-and-libbz2.patch | 109 +++----
debian/patches/add_MEM_F_SELF_OVLP.patch | 15 -
debian/patches/cmake-adj | 23 --
debian/patches/cmake-typo-fixes | 72 +----
debian/patches/dependency-fix | 225 +++++++------
debian/patches/disable-version-check | 8 +-
debian/patches/drop-mathjax | 12 -
debian/patches/jellyfish-update | 106 -------
debian/patches/reproducible-build | 22 --
debian/patches/series | 5 -
debian/patches/use-system-pkg-config-tbb | 10 +-
src/CMakeLists.txt | 22 +-
src/Salmon.cpp | 8 +-
src/SalmonQuantify.cpp | 2 +-
17 files changed, 407 insertions(+), 636 deletions(-)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 0a6ec55..14b9cc8 100755
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -23,7 +23,7 @@ set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/Modules/")
set (WARNING_IGNORE_FLAGS "-Wno-deprecated-register")
set (BOOST_CXX_FLAGS "-Wno-deprecated-register -std=c++11")
## Prefer static to dynamic libraries
-SET(CMAKE_FIND_LIBRARY_SUFFIXES .a ${CMAKE_FIND_LIBRARY_SUFFIXES})
+# SET(CMAKE_FIND_LIBRARY_SUFFIXES .a ${CMAKE_FIND_LIBRARY_SUFFIXES})
## Set the standard required compile flags
# Nov 18th --- removed -DHAVE_CONFIG_H
@@ -176,10 +176,13 @@ endif ( DEFINED CUSTOM_BOOST_PATH )
##
# We want static, multithreaded boost libraries
##
-set (Boost_USE_STATIC_LIBS ON)
+set (Boost_USE_STATIC_LIBS OFF)
set (Boost_USE_MULTITHREADED ON)
#set (Boost_USE_STATIC_RUNTIME OFF)
+find_package (PkgConfig)
+pkg_check_modules(TBB REQUIRED tbb)
+
find_package (ZLIB)
if (NOT ZLIB_FOUND)
message (FATAL_ERROR "zlib must be installed before configuration & building can proceed")
@@ -237,7 +240,7 @@ endif()
# Set the latest version and look for what we need
##
set(Boost_ADDITIONAL_VERSIONS "1.53" "1.53.0" "1.54" "1.55" "1.56" "1.57.0" "1.58" "1.59" "1.60" "1.61")
-find_package(Boost 1.53.0 COMPONENTS iostreams filesystem system thread timer chrono program_options serialization)
+find_package(Boost 1.53.0 COMPONENTS filesystem system thread timer program_options)
message("BOOST_INCLUDEDIR = ${BOOST_INCLUDEDIR}")
message("BOOST_LIBRARYDIR = ${BOOST_LIBRARYDIR}")
message("Boost_FOUND = ${Boost_FOUND}")
@@ -347,152 +350,153 @@ ExternalProject_Add(libdivsufsort
)
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)
-ExternalProject_Add(libcereal
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
- DOWNLOAD_COMMAND curl -k -L https://github.com/USCiLab/cereal/archive/v1.1.2.tar.gz -o cereal-v1.1.2.tar.gz &&
- tar -xzvf cereal-v1.1.2.tar.gz
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/cereal-1.1.2
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- UPDATE_COMMAND sh -c "mkdir -p <SOURCE_DIR>/build"
- BINARY_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/cereal-1.1.2/build
- CONFIGURE_COMMAND ""
- BUILD_COMMAND ""
- INSTALL_COMMAND sh -c "mkdir -p <INSTALL_DIR>/include && cp -r <SOURCE_DIR>/include/cereal <INSTALL_DIR>/include"
-)
-
-message("Build system will fetch and build BWA (for Salmon)")
-message("==================================================================")
-include(ExternalProject)
-ExternalProject_Add(libbwa
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/bwa/archive/0.7.12.3.tar.gz -o bwa-master.tar.gz &&
- mkdir -p bwa-master &&
- tar -xzvf bwa-master.tar.gz --strip-components=1 -C bwa-master
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bwa-master
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- CONFIGURE_COMMAND ""
- BUILD_COMMAND sh -c "make CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}"
- INSTALL_COMMAND sh -c "mkdir -p <INSTALL_DIR>/lib && mkdir -p <INSTALL_DIR>/include/bwa && cp libbwa.a <INSTALL_DIR>/lib && cp *.h <INSTALL_DIR>/include/bwa && cp is.c bwtindex.c bwt_gen.c QSufSort.c ${CMAKE_CURRENT_SOURCE_DIR}/src/"
- BUILD_IN_SOURCE TRUE
-)
-
-find_package(Jellyfish 2.2.6)
-
-if (NOT JELLYFISH_FOUND)
-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/v2.2.6/jellyfish-2.2.6.tar.gz -o jellyfish-2.2.6.tgz &&
- rm -fr jellyfish-2.2.6 &&
- tar -xzvf jellyfish-2.2.6.tgz
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.6
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.6/configure --prefix=<INSTALL_DIR> CC=${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
-)
-endif()
+#message("Build system will fetch and build the Cereal serialization library")
+#message("==================================================================")
+#include(ExternalProject)
+#ExternalProject_Add(libcereal
+# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+# DOWNLOAD_COMMAND curl -k -L https://github.com/USCiLab/cereal/archive/v1.1.2.tar.gz -o cereal-v1.1.2.tar.gz &&
+# tar -xzvf cereal-v1.1.2.tar.gz
+# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/cereal-1.1.2
+# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+# UPDATE_COMMAND sh -c "mkdir -p <SOURCE_DIR>/build"
+# BINARY_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/cereal-1.1.2/build
+# CONFIGURE_COMMAND ""
+# BUILD_COMMAND ""
+# INSTALL_COMMAND sh -c "mkdir -p <INSTALL_DIR>/include && cp -r <SOURCE_DIR>/include/cereal <INSTALL_DIR>/include"
+#)
+#
+#message("Build system will fetch and build BWA (for Salmon)")
+#message("==================================================================")
+#include(ExternalProject)
+#ExternalProject_Add(libbwa
+# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+# DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/bwa/archive/0.7.12.3.tar.gz -o bwa-master.tar.gz &&
+# mkdir -p bwa-master &&
+# tar -xzvf bwa-master.tar.gz --strip-components=1 -C bwa-master
+# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bwa-master
+# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+# CONFIGURE_COMMAND ""
+# BUILD_COMMAND sh -c "make CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}"
+# INSTALL_COMMAND sh -c "mkdir -p <INSTALL_DIR>/lib && mkdir -p <INSTALL_DIR>/include/bwa && cp libbwa.a <INSTALL_DIR>/lib && cp *.h <INSTALL_DIR>/include/bwa && cp is.c bwtindex.c bwt_gen.c QSufSort.c ${CMAKE_CURRENT_SOURCE_DIR}/src/"
+# BUILD_IN_SOURCE TRUE
+#)
+#
+#find_package(Jellyfish 2.2.6)
+#
+#if (NOT JELLYFISH_FOUND)
+#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/v2.2.6/jellyfish-2.2.6.tar.gz -o jellyfish-2.2.6.tgz &&
+# rm -fr jellyfish-2.2.6 &&
+# tar -xzvf jellyfish-2.2.6.tgz
+# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.6
+# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+# CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.6/configure --prefix=<INSTALL_DIR> CC=${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
+#)
+#endif()
+
+#find_package(TBB)
-find_package(TBB)
##
#
# Fetch and build Intel's Threading Building Blocks library.
#
##
-if(NOT TBB_FOUND)
+#if(NOT TBB_FOUND)
-set(TBB_WILL_RECONFIGURE TRUE)
+#set(TBB_WILL_RECONFIGURE TRUE)
# Set the appropriate compiler
-if (CLANG)
- set(TBB_COMPILER "clang")
-else()
- set(TBB_COMPILER "gcc")
-endif()
-
-message("Build system will fetch and build Intel Threading Building Blocks")
-message("==================================================================")
-# These are useful for the custom install step we'll do later
-set(TBB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb44_20160526oss)
-set(TBB_INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install)
-
-if ("${TBB_COMPILER}" STREQUAL "gcc")
+#if (CLANG)
+# set(TBB_COMPILER "clang")
+#else()
+# set(TBB_COMPILER "gcc")
+#endif()
+
+#message("Build system will fetch and build Intel Threading Building Blocks")
+#message("==================================================================")
+## These are useful for the custom install step we'll do later
+#set(TBB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb44_20160526oss)
+#set(TBB_INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install)
+
+#if ("${TBB_COMPILER}" STREQUAL "gcc")
## Don't know why it's a problem yet, but if we're using
## GCC, get rid of the DO_ITT_NOTIFY flag
set(TBB_CXXFLAGS "${TBB_CXXFLAGS} -UDO_ITT_NOTIFY")
-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
- DOWNLOAD_COMMAND curl -k -L https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160526oss_src_0.tgz -o tbb_20160526oss_src.tgz &&
- tar -xzvf tbb_20160526oss_src.tgz
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb44_20160526oss
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- PATCH_COMMAND "${TBB_PATCH_STEP}"
- CONFIGURE_COMMAND ""
- BUILD_COMMAND make CXXFLAGS=${TBB_CXXFLAGS} lambdas=1 compiler=${TBB_COMPILER} cfg=release tbb_build_prefix=LIBS
- 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
-)
-
-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}
- DEPENDEES install
-)
-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
+# DOWNLOAD_COMMAND curl -k -L https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160526oss_src_0.tgz -o tbb_20160526oss_src.tgz &&
+# tar -xzvf tbb_20160526oss_src.tgz
+# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb44_20160526oss
+# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+# PATCH_COMMAND "${TBB_PATCH_STEP}"
+# CONFIGURE_COMMAND ""
+# BUILD_COMMAND make CXXFLAGS=${TBB_CXXFLAGS} lambdas=1 compiler=${TBB_COMPILER} cfg=release tbb_build_prefix=LIBS
+# 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
+#)
+
+#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}
+# DEPENDEES install
+#)
+#endif()
##
# If we're fetching tbb, we need to have dummy paths for these variables
# so that CMake won't complain
##
-if(TBB_WILL_RECONFIGURE)
- set(TBB_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
- set(TBB_LIBRARY_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib)
- #set(TBB_LIBRARIES tbb tbbmalloc)
- set(TBB_LIBRARIES ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib/libtbb.${SHARED_LIB_EXTENSION}
- ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib/libtbbmalloc.${SHARED_LIB_EXTENSION}
- )
-endif()
+#if(TBB_WILL_RECONFIGURE)
+# set(TBB_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
+# set(TBB_LIBRARY_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib)
+# #set(TBB_LIBRARIES tbb tbbmalloc)
+# set(TBB_LIBRARIES ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib/libtbb.${SHARED_LIB_EXTENSION}
+# ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib/libtbbmalloc.${SHARED_LIB_EXTENSION}
+# )
+#endif()
##
# Similar to the Boost trick above, the libtbb reconfigure should force this code
# to be run on the second configuration pass, where it should appropriately set the
# TBB_INSTALL_DIR variable.
##
-if (TBB_RECONFIGURE)
- unset(TBB_FOUND CACHE)
- unset(TBB_INSTALL_DIR CACHE)
- unset(CMAKE_PREFIX_PATH CACHE)
- set(CMAKE_PREFIX_PATH ${CMAKE_CURRENT_SOURCE_DIR}/external/install)
- set(TBB_INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install)
- message("TBB_INSTALL_DIR = ${TBB_INSTALL_DIR}")
- find_package(TBB)
-endif()
+#if (TBB_RECONFIGURE)
+# unset(TBB_FOUND CACHE)
+# unset(TBB_INSTALL_DIR CACHE)
+# unset(CMAKE_PREFIX_PATH CACHE)
+# set(CMAKE_PREFIX_PATH ${CMAKE_CURRENT_SOURCE_DIR}/external/install)
+# set(TBB_INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install)
+# message("TBB_INSTALL_DIR = ${TBB_INSTALL_DIR}")
+# find_package(TBB)
+#endif()
message("TBB_LIBRARIES = ${TBB_LIBRARIES}")
-message("Build system will compile libgff")
-message("==================================================================")
-ExternalProject_Add(libgff
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
- DOWNLOAD_COMMAND curl -k -L https://github.com/Kingsford-Group/libgff/archive/v1.0.tar.gz -o libgff.tgz &&
- tar -xzvf libgff.tgz &&
- rm -fr libgff &&
- mv libgff-1.0 libgff
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libgff
- UPDATE_COMMAND sh -c "mkdir -p <SOURCE_DIR>/build"
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- BINARY_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libgff/build
- CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_CURRENT_SOURCE_DIR}/external/install
-)
+#message("Build system will compile libgff")
+#message("==================================================================")
+#ExternalProject_Add(libgff
+# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+# DOWNLOAD_COMMAND curl -k -L https://github.com/Kingsford-Group/libgff/archive/v1.0.tar.gz -o libgff.tgz &&
+# tar -xzvf libgff.tgz &&
+# rm -fr libgff &&
+# mv libgff-1.0 libgff
+# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libgff
+# UPDATE_COMMAND sh -c "mkdir -p <SOURCE_DIR>/build"
+# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+# BINARY_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libgff/build
+# CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_CURRENT_SOURCE_DIR}/external/install
+#)
# Because of the way that Apple has changed SIP
# in el capitan, some headers may be in a new location
@@ -502,39 +506,39 @@ if (APPLE)
endif()
-message("Build system will compile Staden IOLib")
-message("==================================================================")
-ExternalProject_Add(libstadenio
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/staden-io_lib/releases/download/v1.13.10/io_lib-1.13.10.tar.gz -o staden-io_lib-v1.13.10.tar.gz &&
- mkdir -p staden-io_lib-1.13.10 &&
- tar -xzf staden-io_lib-v1.13.10.tar.gz --strip-components=1 -C staden-io_lib-1.13.10 &&
- rm -fr staden-io_lib &&
- mv -f staden-io_lib-1.13.10 staden-io_lib
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/staden-io_lib
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- CONFIGURE_COMMAND ./configure --enable-shared=no --without-libcurl --prefix=<INSTALL_DIR> LDFLAGS=${LIBSTADEN_LDFLAGS} CFLAGS=${LIBSTADEN_CFLAGS} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
- BUILD_COMMAND make CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CFLAGS+=${STADEN_INC} CFLAGS+=${STADEN_LIB}
-
- BUILD_IN_SOURCE 1
- INSTALL_COMMAND make install
-)
-
-message("Build system will fetch SPDLOG")
-message("==================================================================")
-ExternalProject_Add(libspdlog
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/spdlog/archive/v1.0.1.tar.gz -o spdlog-v1.0.1.tar.gz &&
- tar -xzf spdlog-v1.0.1.tar.gz &&
- rm -fr spdlog &&
- mv -f spdlog-1.0.1 spdlog
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/spdlog
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- CONFIGURE_COMMAND ""
- BUILD_COMMAND ""
- BUILD_IN_SOURCE 1
- INSTALL_COMMAND cp -r <SOURCE_DIR>/include/spdlog <INSTALL_DIR>/include
-)
+#message("Build system will compile Staden IOLib")
+#message("==================================================================")
+#ExternalProject_Add(libstadenio
+# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+# DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/staden-io_lib/releases/download/v1.13.10/io_lib-1.13.10.tar.gz -o staden-io_lib-v1.13.10.tar.gz &&
+# mkdir -p staden-io_lib-1.13.10 &&
+# tar -xzf staden-io_lib-v1.13.10.tar.gz --strip-components=1 -C staden-io_lib-1.13.10 &&
+# rm -fr staden-io_lib &&
+# mv -f staden-io_lib-1.13.10 staden-io_lib
+# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/staden-io_lib
+# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+# CONFIGURE_COMMAND ./configure --enable-shared=no --without-libcurl --prefix=<INSTALL_DIR> LDFLAGS=${LIBSTADEN_LDFLAGS} CFLAGS=${LIBSTADEN_CFLAGS} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
+# BUILD_COMMAND make CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CFLAGS+=${STADEN_INC} CFLAGS+=${STADEN_LIB}
+#
+# BUILD_IN_SOURCE 1
+# INSTALL_COMMAND make install
+#)
+
+#message("Build system will fetch SPDLOG")
+#message("==================================================================")
+#ExternalProject_Add(libspdlog
+# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+# DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/spdlog/archive/v1.0.1.tar.gz -o spdlog-v1.0.1.tar.gz &&
+# tar -xzf spdlog-v1.0.1.tar.gz &&
+# rm -fr spdlog &&
+# mv -f spdlog-1.0.1 spdlog
+# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/spdlog
+# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+# CONFIGURE_COMMAND ""
+# BUILD_COMMAND ""
+# BUILD_IN_SOURCE 1
+# INSTALL_COMMAND cp -r <SOURCE_DIR>/include/spdlog <INSTALL_DIR>/include
+#)
set (FAST_MALLOC_LIB "")
set (HAVE_FAST_MALLOC FALSE)
@@ -558,23 +562,23 @@ if (NOT HAVE_FAST_MALLOC)
endif()
endif()
-if (NOT HAVE_FAST_MALLOC)
- message("Build system will fetch and use JEMalloc")
- message("==================================================================")
- ExternalProject_Add(libjemalloc
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/jemalloc/archive/4.0.4.tar.gz -o jemalloc-4.0.4.tar.gz &&
- tar -xzf jemalloc-4.0.4.tar.gz
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jemalloc-4.0.4
- BUILD_IN_SOURCE TRUE
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- CONFIGURE_COMMAND sh -c "CC=${CMAKE_C_COMPILER} ./autogen.sh --prefix=<INSTALL_DIR>"
- INSTALL_COMMAND cp -r lib <INSTALL_DIR>/ && cp -r include <INSTALL_DIR>/
- )
-
- set (FAST_MALLOC_LIB ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib/libjemalloc.a)
- set (HAVE_FAST_MALLOC TRUE)
-endif ()
+#if (NOT HAVE_FAST_MALLOC)
+# message("Build system will fetch and use JEMalloc")
+# message("==================================================================")
+# ExternalProject_Add(libjemalloc
+# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+# DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/jemalloc/archive/4.0.4.tar.gz -o jemalloc-4.0.4.tar.gz &&
+# tar -xzf jemalloc-4.0.4.tar.gz
+# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jemalloc-4.0.4
+# BUILD_IN_SOURCE TRUE
+# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+# CONFIGURE_COMMAND sh -c "CC=${CMAKE_C_COMPILER} ./autogen.sh --prefix=<INSTALL_DIR>"
+# INSTALL_COMMAND cp -r lib <INSTALL_DIR>/ && cp -r include <INSTALL_DIR>/
+# )
+#
+# set (FAST_MALLOC_LIB ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib/libjemalloc.a)
+# set (HAVE_FAST_MALLOC TRUE)
+#endif ()
##
diff --git a/debian/patches/0007-Remove-unnecessarily-linked-libraries.patch b/debian/patches/0007-Remove-unnecessarily-linked-libraries.patch
index f29f1a9..0f1e7a5 100644
--- a/debian/patches/0007-Remove-unnecessarily-linked-libraries.patch
+++ b/debian/patches/0007-Remove-unnecessarily-linked-libraries.patch
@@ -7,25 +7,10 @@ Subject: Remove unnecessarily linked libraries
src/CMakeLists.txt | 6 +-----
2 files changed, 2 insertions(+), 6 deletions(-)
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 378eb83..bd6393b 100755
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -226,7 +226,7 @@ endif()
- # Set the latest version and look for what we need
- ##
- set(Boost_ADDITIONAL_VERSIONS "1.53" "1.53.0" "1.54" "1.55" "1.56" "1.57.0" "1.58")
--find_package(Boost 1.53.0 COMPONENTS iostreams filesystem system thread timer chrono program_options serialization)
-+find_package(Boost 1.53.0 COMPONENTS filesystem system thread program_options)
- message("BOOST_INCLUDEDIR = ${BOOST_INCLUDEDIR}")
- message("BOOST_LIBRARYDIR = ${BOOST_LIBRARYDIR}")
- message("Boost_FOUND = ${Boost_FOUND}")
-diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
-index 3f300c8..df31909 100755
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
-@@ -112,16 +112,12 @@ target_link_libraries(salmon
- libjellyfish-2.0.so
+@@ -134,16 +134,12 @@ target_link_libraries(salmon
+ libjellyfish-2.0.so
/usr/lib/libbwa.a
m
- ${LIBLZMA_LIBRARIES}
@@ -39,6 +24,17 @@ index 3f300c8..df31909 100755
-add_dependencies(salmon libbwa)
-
+ # Link the executable
+ target_link_libraries(unitTests
+ salmon_core
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -240,7 +240,7 @@ endif()
+ # Set the latest version and look for what we need
##
- # This ensures that the salmon executable should work with or without `make install`
- ##
+ set(Boost_ADDITIONAL_VERSIONS "1.53" "1.53.0" "1.54" "1.55" "1.56" "1.57.0" "1.58" "1.59" "1.60" "1.61")
+-find_package(Boost 1.53.0 COMPONENTS iostreams filesystem system thread timer chrono program_options serialization)
++find_package(Boost 1.53.0 COMPONENTS filesystem system thread timer program_options)
+ message("BOOST_INCLUDEDIR = ${BOOST_INCLUDEDIR}")
+ message("BOOST_LIBRARYDIR = ${BOOST_LIBRARYDIR}")
+ message("Boost_FOUND = ${Boost_FOUND}")
diff --git a/debian/patches/0008-Remove-salmon_core-lib.patch b/debian/patches/0008-Remove-salmon_core-lib.patch
index 6eed4e6..508f7ec 100644
--- a/debian/patches/0008-Remove-salmon_core-lib.patch
+++ b/debian/patches/0008-Remove-salmon_core-lib.patch
@@ -6,13 +6,11 @@ Subject: Remove salmon_core lib
src/CMakeLists.txt | 8 ++------
1 file changed, 2 insertions(+), 6 deletions(-)
-diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
-index df31909..346d507 100755
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
-@@ -73,11 +73,8 @@ endif()
-
- set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
+@@ -102,11 +102,8 @@ else()
+ set(CMAKE_INSTALL_RPATH_USE_LINK_PATH FALSE)
+ endif()
-# Build the Salmon library
-add_library(salmon_core ${SALMON_LIB_SRCS} )
@@ -21,22 +19,22 @@ index df31909..346d507 100755
-add_executable(salmon ${SALMON_MAIN_SRCS} ${SALMON_ALIGN_SRCS})
+add_executable(salmon ${SALMON_LIB_SRCS} ${SALMON_MAIN_SRCS} ${SALMON_ALIGN_SRCS})
- #add_executable(salmon-read ${SALMON_READ_SRCS})
- #set_target_properties(salmon-read PROPERTIES COMPILE_FLAGS "${CMAKE_CXX_FLAGS} -DHAVE_LIBPTHREAD -D_PBGZF_USE -fopenmp"
-@@ -103,7 +100,6 @@ endif()
+ add_executable(unitTests ${UNIT_TESTS_SRCS})
+
+@@ -123,7 +120,6 @@ set (SUFFARRAY64_LIB ${GAT_SOURCE_DIR}/e
# Link the executable
target_link_libraries(salmon
-- salmon_core
+- salmon_core
gff
${PTHREAD_LIB}
- ${Boost_LIBRARIES}
-@@ -158,7 +154,7 @@ endif()
+ ${Boost_LIBRARIES}
+@@ -217,7 +213,7 @@ install(DIRECTORY
# install(FILES ${Boost_LIBRARIES}
# DESTINATION ${INSTALL_LIB_DIR})
-install(TARGETS salmon salmon_core
+install(TARGETS salmon
- RUNTIME DESTINATION bin
+ RUNTIME DESTINATION bin
LIBRARY DESTINATION lib
ARCHIVE DESTINATION lib
diff --git a/debian/patches/0009-Remove-FIND_PACKAGE-for-liblzma-and-libbz2.patch b/debian/patches/0009-Remove-FIND_PACKAGE-for-liblzma-and-libbz2.patch
index 9c0a473..09ae7fe 100644
--- a/debian/patches/0009-Remove-FIND_PACKAGE-for-liblzma-and-libbz2.patch
+++ b/debian/patches/0009-Remove-FIND_PACKAGE-for-liblzma-and-libbz2.patch
@@ -7,11 +7,9 @@ As these seem not to be required.
CMakeLists.txt | 94 +++++++++++++++++++++++++++++-----------------------------
1 file changed, 47 insertions(+), 47 deletions(-)
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index bd6393b..0f320f1 100755
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-@@ -174,53 +174,53 @@ if (NOT ZLIB_FOUND)
+@@ -188,53 +188,53 @@ if (NOT ZLIB_FOUND)
message (FATAL_ERROR "zlib must be installed before configuration & building can proceed")
endif()
@@ -21,16 +19,30 @@ index bd6393b..0f320f1 100755
- message ("=======================================")
-ExternalProject_Add(liblzma
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- URL http://tukaani.org/xz/xz-5.2.0.tar.gz
-- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.0
+- URL http://tukaani.org/xz/xz-5.2.2.tar.gz
+- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.2
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- BUILD_IN_SOURCE TRUE
-- CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.0/configure --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
+- CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.2/configure --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
- BUILD_COMMAND make
- INSTALL_COMMAND make install
-)
--# Tell cmake that the external project generated a library so we can
--# add dependencies here instead of later
++#find_package (LibLZMA)
++#if (NOT LIBLZMA_FOUND)
++# message ("Will attempt to fetch and build liblzma")
++# message ("=======================================")
++#ExternalProject_Add(liblzma
++# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
++# URL http://tukaani.org/xz/xz-5.2.2.tar.gz
++# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.2
++# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
++# BUILD_IN_SOURCE TRUE
++# CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.2/configure --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
++# BUILD_COMMAND make
++# INSTALL_COMMAND make install
++#)
+ # Tell cmake that the external project generated a library so we can
+ # add dependencies here instead of later
-set (LIBLZMA_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/liblzma.a)
-set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib")
-set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include")
@@ -38,7 +50,14 @@ index bd6393b..0f320f1 100755
- message("Found liblzma library: ${LIBLZMA_LIBRARIES}")
- message("===========================================")
-endif()
--
++#set (LIBLZMA_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/liblzma.a)
++#set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib")
++#set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include")
++#else()
++# message("Found liblzma library: ${LIBLZMA_LIBRARIES}")
++# message("===========================================")
++#endif()
+
-find_package (BZip2)
-if (NOT BZIP2_FOUND)
- message ("Will attempt to fetch and build libbz2")
@@ -53,8 +72,22 @@ index bd6393b..0f320f1 100755
- BUILD_COMMAND make CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
- INSTALL_COMMAND make install PREFIX=<INSTALL_DIR>
-)
--# Tell cmake that the external project generated a library so we can
--# add dependencies here instead of later
++#find_package (BZip2)
++#if (NOT BZIP2_FOUND)
++# message ("Will attempt to fetch and build libbz2")
++# message ("=======================================")
++#ExternalProject_Add(libbz2
++# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
++# URL http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz
++# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bzip2-1.0.6
++# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
++# BUILD_IN_SOURCE TRUE
++# CONFIGURE_COMMAND ""
++# BUILD_COMMAND make CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
++# INSTALL_COMMAND make install PREFIX=<INSTALL_DIR>
++#)
+ # Tell cmake that the external project generated a library so we can
+ # add dependencies here instead of later
-set (BZIP2_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/libbz2.a)
-set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib -I${GAT_SOURCE_DIR}/external/install/include")
-set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include")
@@ -62,53 +95,13 @@ index bd6393b..0f320f1 100755
- message("Found libbz2 library: ${BZIP2_LIBRARIES}")
- message("===========================================")
-endif()
-+# find_package (LibLZMA)
-+# if (NOT LIBLZMA_FOUND)
-+# message ("Will attempt to fetch and build liblzma")
-+# message ("=======================================")
-+# ExternalProject_Add(liblzma
-+# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-+# URL http://tukaani.org/xz/xz-5.2.0.tar.gz
-+# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.0
-+# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-+# BUILD_IN_SOURCE TRUE
-+# CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.0/configure --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
-+# BUILD_COMMAND make
-+# INSTALL_COMMAND make install
-+# )
-+# # Tell cmake that the external project generated a library so we can
-+# # add dependencies here instead of later
-+# set (LIBLZMA_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/liblzma.a)
-+# set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib")
-+# set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include")
-+# else()
-+# message("Found liblzma library: ${LIBLZMA_LIBRARIES}")
-+# message("===========================================")
-+# endif()
-+
-+# find_package (BZip2)
-+# if (NOT BZIP2_FOUND)
-+# message ("Will attempt to fetch and build libbz2")
-+# message ("=======================================")
-+# ExternalProject_Add(libbz2
-+# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-+# URL http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz
-+# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bzip2-1.0.6
-+# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-+# BUILD_IN_SOURCE TRUE
-+# CONFIGURE_COMMAND ""
-+# BUILD_COMMAND make CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
-+# INSTALL_COMMAND make install PREFIX=<INSTALL_DIR>
-+# )
-+# # Tell cmake that the external project generated a library so we can
-+# # add dependencies here instead of later
-+# set (BZIP2_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/libbz2.a)
-+# set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib -I${GAT_SOURCE_DIR}/external/install/include")
-+# set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include")
-+# else()
-+# message("Found libbz2 library: ${BZIP2_LIBRARIES}")
-+# message("===========================================")
-+# endif()
++#set (BZIP2_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/libbz2.a)
++#set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib -I${GAT_SOURCE_DIR}/external/install/include")
++#set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include")
++#else()
++# message("Found libbz2 library: ${BZIP2_LIBRARIES}")
++# message("===========================================")
++#endif()
##
# Set the latest version and look for what we need
diff --git a/debian/patches/add_MEM_F_SELF_OVLP.patch b/debian/patches/add_MEM_F_SELF_OVLP.patch
deleted file mode 100644
index 320fc13..0000000
--- a/debian/patches/add_MEM_F_SELF_OVLP.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Description: redefine MEM_F_SELF_OVLP
- libbwa upstream has dropped MEM_F_SELF_OVLP in their commit
- 1247dc234668c1d7357fa6343222e9b5730e832d. This patch re-introduces this
- definition to fix an FTBFS.
-Author: Sascha Steinbiss <sascha at steinbiss.name>
---- a/src/SalmonQuantify.cpp
-+++ b/src/SalmonQuantify.cpp
-@@ -131,6 +131,7 @@
- /******* STUFF THAT IS STATIC IN BWAMEM THAT WE NEED HERE --- Just re-define it *************/
- #define intv_lt(a, b) ((a).info < (b).info)
- KSORT_INIT(mem_intv, bwtintv_t, intv_lt)
-+#define MEM_F_SELF_OVLP 0x40
-
- typedef struct {
- bwtintv_v mem, mem1, *tmpv[2];
diff --git a/debian/patches/cmake-adj b/debian/patches/cmake-adj
deleted file mode 100644
index fc49091..0000000
--- a/debian/patches/cmake-adj
+++ /dev/null
@@ -1,23 +0,0 @@
-Author: Michael R. Crusoe <crusoe at ucdavis.edu>
-Description: Use the symbolic name for the build directory, don't hardcode it
-Forwarded: https://github.com/COMBINE-lab/salmon/pull/17
---- salmon.orig/cmake/TestSalmon.cmake
-+++ salmon/cmake/TestSalmon.cmake
-@@ -7,7 +7,7 @@
- message(FATAL_ERROR "Error untarring sample_data.tgz")
- endif()
-
--set(SALMON_INDEX_CMD ${TOPLEVEL_DIR}/build/src/salmon index -t transcripts.fasta -i sample_salmon_index)
-+set(SALMON_INDEX_CMD ${CMAKE_BINARY_DIR}/salmon index -t transcripts.fasta -i sample_salmon_index)
- execute_process(COMMAND ${SALMON_INDEX_CMD}
- WORKING_DIRECTORY ${TOPLEVEL_DIR}/sample_data
- RESULT_VARIABLE SALMON_INDEX_RESULT
-@@ -17,7 +17,7 @@
- message(FATAL_ERROR "Error running ${SALMON_INDEX_COMMAND}")
- endif()
-
--set(SALMON_QUANT_COMMAND ${TOPLEVEL_DIR}/build/src/salmon quant -i sample_salmon_index -l IU -1 reads_1.fastq -2 reads_2.fastq -o sample_salmon_quant -n 1000000)
-+set(SALMON_QUANT_COMMAND ${CMAKE_BINARY_DIR}/salmon quant -i sample_salmon_index -l IU -1 reads_1.fastq -2 reads_2.fastq -o sample_salmon_quant -n 1000000)
- execute_process(COMMAND ${SALMON_QUANT_COMMAND}
- WORKING_DIRECTORY ${TOPLEVEL_DIR}/sample_data
- RESULT_VARIABLE SALMON_QUANT_RESULT
diff --git a/debian/patches/cmake-typo-fixes b/debian/patches/cmake-typo-fixes
index fbdd368..4c9a96d 100644
--- a/debian/patches/cmake-typo-fixes
+++ b/debian/patches/cmake-typo-fixes
@@ -1,63 +1,13 @@
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Description: fix upstream's typos
---- salmon.orig/CMakeLists.txt
-+++ salmon/CMakeLists.txt
-@@ -6,12 +6,12 @@
-
- set(CPACK_PACKAGE_VERSION "0.4.2")
- set(CPACK_PACKAGE_VERSION_MAJOR "0")
--set(CPACK_PACKAGE_VERSION_MINOR 4")
--set(CPACK_PACKAGE_VERSION_PATCH 2")
-+set(CPACK_PACKAGE_VERSION_MINOR "4")
-+set(CPACK_PACKAGE_VERSION_PATCH "2")
- set(CPACK_GENERATOR "TGZ")
- set(CPACK_SOURCE_GENERATOR "TGZ")
--set(CPACK_PACKAGE_VENDOR Stony Brook University")
--set(CPACK_PACKAGE_DESCRIPTION_SUMMARY Salmon - Wicked-fast RNA-seq isoform quantification using lightweight alignments")
-+set(CPACK_PACKAGE_VENDOR "Stony Brook University")
-+set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Salmon - Wicked-fast RNA-seq isoform quantification using lightweight alignments")
- set(CPACK_PACKAGE_NAME
- "${CMAKE_PROJECT_NAME}-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}")
- set(CPACK_SOURCE_PACKAGE_FILE_NAME
---- salmon.orig/include/tensemble/GBMRegressor.h
-+++ salmon/include/tensemble/GBMRegressor.h
-@@ -63,7 +63,7 @@
- if (loss_function==SQUARE_LOSS) {
- loss=new SquareLoss();
- }else {
-- fprintf(stderr, "Error: Unknow loss function\n");
-+ fprintf(stderr, "Error: Unknown loss function\n");
- return ENSEMBLE_FAIL;
- }
- //allocate memory for prior and trees
---- salmon.orig/include/tensemble/cmdline.h
-+++ salmon/include/tensemble/cmdline.h
-@@ -91,7 +91,7 @@
- value[s] = "";
- }
- } else {
-- fprintf(stderr, "Error: Unknow parameter %s.\n",s.c_str());
-+ fprintf(stderr, "Error: Unknown parameter %s.\n",s.c_str());
- print_help();
- return false;
- }
-@@ -135,7 +135,7 @@
- }
- }
- if (i==len) {
-- fprintf(stderr, "Error: Unknow parameter %s.\n",iter->first.c_str());
-+ fprintf(stderr, "Error: Unknown parameter %s.\n",iter->first.c_str());
- // print_help();
- return false;
- }
---- salmon.orig/src/SalmonQuantify.cpp
-+++ salmon/src/SalmonQuantify.cpp
-@@ -2928,7 +2928,7 @@
- "many reads, then just keep the data in memory for subsequent rounds of inference. Obviously, this value should "
- "not be too large if you wish to keep a low memory usage, but setting it large enough can substantially speed up "
- "inference on \"small\" files that contain only a few million reads.")
-- ("maxOcc,m", po::value<int>(&(memOptions->max_occ))->default_value(200), "(S)MEMs occuring more than this many times won't be considered.")
-+ ("maxOcc,m", po::value<int>(&(memOptions->max_occ))->default_value(200), "(S)MEMs occurring more than this many times won't be considered.")
- ("maxReadOcc,w", po::value<uint32_t>(&(sopt.maxReadOccs))->default_value(100), "Reads \"mapping\" to more than this many places won't be considered.")
- ("noEffectiveLengthCorrection", po::bool_switch(&(sopt.noEffectiveLengthCorrection))->default_value(false), "Disables "
- "effective length correction when computing the probability that a fragment was generated "
+--- a/src/SalmonQuantify.cpp
++++ b/src/SalmonQuantify.cpp
+@@ -1985,7 +1985,7 @@ int salmonQuantify(int argc, char* argv[
+ (
+ "maxOcc,m",
+ po::value<int>(&(memOptions->max_occ))->default_value(200),
+- "(S)MEMs occuring more than this many times won't be considered.")
++ "(S)MEMs occurring more than this many times won't be considered.")
+ (
+ "initUniform", po::bool_switch(&(sopt.initUniform))->default_value(false),
+ "initialize the offline inference with uniform parameters, rather than seeding with online parameters.")
diff --git a/debian/patches/dependency-fix b/debian/patches/dependency-fix
index 757a267..20a4735 100644
--- a/debian/patches/dependency-fix
+++ b/debian/patches/dependency-fix
@@ -1,17 +1,17 @@
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Description: Use Debian version of dependencies, don't download them
---- salmon.orig/CMakeLists.txt
-+++ salmon/CMakeLists.txt
-@@ -22,7 +22,7 @@
- set (WARNING_IGNORE_FLAGS "-Wno-deprecated-register")
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -23,7 +23,7 @@ set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PAT
+ set (WARNING_IGNORE_FLAGS "-Wno-deprecated-register")
set (BOOST_CXX_FLAGS "-Wno-deprecated-register -std=c++11")
## Prefer static to dynamic libraries
-SET(CMAKE_FIND_LIBRARY_SUFFIXES .a ${CMAKE_FIND_LIBRARY_SUFFIXES})
+# SET(CMAKE_FIND_LIBRARY_SUFFIXES .a ${CMAKE_FIND_LIBRARY_SUFFIXES})
## Set the standard required compile flags
- # Nov 18th --- removed -DHAVE_CONFIG_H
-@@ -165,7 +165,7 @@
+ # Nov 18th --- removed -DHAVE_CONFIG_H
+@@ -176,7 +176,7 @@ endif ( DEFINED CUSTOM_BOOST_PATH )
##
# We want static, multithreaded boost libraries
##
@@ -20,20 +20,21 @@ Description: Use Debian version of dependencies, don't download them
set (Boost_USE_MULTITHREADED ON)
#set (Boost_USE_STATIC_RUNTIME OFF)
-@@ -322,51 +322,53 @@
-
- set(EXTERNAL_LIBRARY_PATH $CMAKE_CURRENT_SOURCE_DIR/lib)
+@@ -347,56 +347,56 @@ ExternalProject_Add(libdivsufsort
+ )
+ 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)
-ExternalProject_Add(libcereal
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- URL http://www.cs.cmu.edu/~robp/files/cereal-v1.0.0.tgz
-- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/cereal-1.0.0
+- DOWNLOAD_COMMAND curl -k -L https://github.com/USCiLab/cereal/archive/v1.1.2.tar.gz -o cereal-v1.1.2.tar.gz &&
+- tar -xzvf cereal-v1.1.2.tar.gz
+- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/cereal-1.1.2
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- UPDATE_COMMAND sh -c "mkdir -p <SOURCE_DIR>/build"
-- BINARY_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/cereal-1.0.0/build
+- BINARY_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/cereal-1.1.2/build
- CONFIGURE_COMMAND ""
- BUILD_COMMAND ""
- INSTALL_COMMAND sh -c "mkdir -p <INSTALL_DIR>/include && cp -r <SOURCE_DIR>/include/cereal <INSTALL_DIR>/include"
@@ -45,8 +46,8 @@ Description: Use Debian version of dependencies, don't download them
-ExternalProject_Add(libbwa
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/bwa/archive/0.7.12.3.tar.gz -o bwa-master.tar.gz &&
-- mkdir -p bwa-master &&
-- tar -xzvf bwa-master.tar.gz --strip-components=1 -C bwa-master
+- mkdir -p bwa-master &&
+- tar -xzvf bwa-master.tar.gz --strip-components=1 -C bwa-master
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bwa-master
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- CONFIGURE_COMMAND ""
@@ -55,45 +56,48 @@ Description: Use Debian version of dependencies, don't download them
- BUILD_IN_SOURCE TRUE
-)
-
+-find_package(Jellyfish 2.2.6)
+-
+-if (NOT JELLYFISH_FOUND)
-message("Build system will fetch and build Jellyfish")
-message("==================================================================")
-ExternalProject_Add(libjellyfish
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- URL ftp://ftp.genome.umd.edu/pub/jellyfish/jellyfish-2.1.3.tar.gz
-- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.1.3
+- DOWNLOAD_COMMAND curl -k -L https://github.com/gmarcais/Jellyfish/releases/download/v2.2.6/jellyfish-2.2.6.tar.gz -o jellyfish-2.2.6.tgz &&
+- rm -fr jellyfish-2.2.6 &&
+- tar -xzvf jellyfish-2.2.6.tgz
+- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.6
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-- CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.1.3/configure --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${JELLYFISH_CXX_FLAGS}
+- CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.6/configure --prefix=<INSTALL_DIR> CC=${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-2.1.3/jellyfish/ &&
-- cp config.h <INSTALL_DIR>/include/
+- INSTALL_COMMAND make install
-)
+-endif()
+#message("Build system will fetch and build the Cereal serialization library")
+#message("==================================================================")
+#include(ExternalProject)
+#ExternalProject_Add(libcereal
+# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-+# URL http://www.cs.cmu.edu/~robp/files/cereal-v1.0.0.tgz
-+# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/cereal-1.0.0
++# DOWNLOAD_COMMAND curl -k -L https://github.com/USCiLab/cereal/archive/v1.1.2.tar.gz -o cereal-v1.1.2.tar.gz &&
++# tar -xzvf cereal-v1.1.2.tar.gz
++# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/cereal-1.1.2
+# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+# UPDATE_COMMAND sh -c "mkdir -p <SOURCE_DIR>/build"
-+# BINARY_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/cereal-1.0.0/build
++# BINARY_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/cereal-1.1.2/build
+# CONFIGURE_COMMAND ""
+# BUILD_COMMAND ""
+# INSTALL_COMMAND sh -c "mkdir -p <INSTALL_DIR>/include && cp -r <SOURCE_DIR>/include/cereal <INSTALL_DIR>/include"
+#)
-+
-+#find_package(bwa)
-+
++#
+#message("Build system will fetch and build BWA (for Salmon)")
+#message("==================================================================")
+#include(ExternalProject)
+#ExternalProject_Add(libbwa
+# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+# DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/bwa/archive/0.7.12.3.tar.gz -o bwa-master.tar.gz &&
-+# mkdir -p bwa-master &&
-+# tar -xzvf bwa-master.tar.gz --strip-components=1 -C bwa-master
++# mkdir -p bwa-master &&
++# tar -xzvf bwa-master.tar.gz --strip-components=1 -C bwa-master
+# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bwa-master
+# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+# CONFIGURE_COMMAND ""
@@ -101,25 +105,29 @@ Description: Use Debian version of dependencies, don't download them
+# INSTALL_COMMAND sh -c "mkdir -p <INSTALL_DIR>/lib && mkdir -p <INSTALL_DIR>/include/bwa && cp libbwa.a <INSTALL_DIR>/lib && cp *.h <INSTALL_DIR>/include/bwa && cp is.c bwtindex.c bwt_gen.c QSufSort.c ${CMAKE_CURRENT_SOURCE_DIR}/src/"
+# BUILD_IN_SOURCE TRUE
+#)
-+
++#
++#find_package(Jellyfish 2.2.6)
++#
++#if (NOT JELLYFISH_FOUND)
+#message("Build system will fetch and build Jellyfish")
+#message("==================================================================")
+#ExternalProject_Add(libjellyfish
+# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-+# URL ftp://ftp.genome.umd.edu/pub/jellyfish/jellyfish-2.1.3.tar.gz
-+# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.1.3
++# DOWNLOAD_COMMAND curl -k -L https://github.com/gmarcais/Jellyfish/releases/download/v2.2.6/jellyfish-2.2.6.tar.gz -o jellyfish-2.2.6.tgz &&
++# rm -fr jellyfish-2.2.6 &&
++# tar -xzvf jellyfish-2.2.6.tgz
++# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.6
+# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-+# CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.1.3/configure --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${JELLYFISH_CXX_FLAGS}
++# CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.6/configure --prefix=<INSTALL_DIR> CC=${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-2.1.3/jellyfish/ &&
-+# cp config.h <INSTALL_DIR>/include/
++# INSTALL_COMMAND make install
+#)
++#endif()
find_package(TBB)
-@@ -375,124 +377,124 @@
+@@ -405,94 +405,94 @@ find_package(TBB)
# Fetch and build Intel's Threading Building Blocks library.
#
##
@@ -134,6 +142,12 @@ Description: Use Debian version of dependencies, don't download them
-else()
- set(TBB_COMPILER "gcc")
-endif()
+-
+-message("Build system will fetch and build Intel Threading Building Blocks")
+-message("==================================================================")
+-# These are useful for the custom install step we'll do later
+-set(TBB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb44_20160526oss)
+-set(TBB_INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install)
+#if (CLANG)
+# set(TBB_COMPILER "clang")
+#else()
@@ -143,36 +157,29 @@ Description: Use Debian version of dependencies, don't download them
+#message("Build system will fetch and build Intel Threading Building Blocks")
+#message("==================================================================")
+## These are useful for the custom install step we'll do later
-+#set(TBB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb43_20140724oss)
++#set(TBB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb44_20160526oss)
+#set(TBB_INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install)
--message("Build system will fetch and build Intel Threading Building Blocks")
--message("==================================================================")
--# These are useful for the custom install step we'll do later
--set(TBB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb43_20140724oss)
--set(TBB_INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install)
--
--if ("${TBB_COMPILER}" STREQUAL "gcc")
-+#if ("${TBB_COMPILER}" STREQUAL "gcc")
+-if ("${TBB_COMPILER}" STREQUAL "gcc")
++#if ("${TBB_COMPILER}" STREQUAL "gcc")
## Don't know why it's a problem yet, but if we're using
## GCC, get rid of the DO_ITT_NOTIFY flag
-- set(TBB_CXXFLAGS "${TBB_CXXFLAGS} -UDO_ITT_NOTIFY")
+ set(TBB_CXXFLAGS "${TBB_CXXFLAGS} -UDO_ITT_NOTIFY")
-endif()
-
-ExternalProject_Add(libtbb
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- URL http://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb43_20140724oss_src.tgz
-- DOWNLOAD_COMMAND curl -k -L http://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb43_20140724oss_src.tgz -o tbb_20140724oss_src.tgz &&
-- tar -xzvf tbb_20140724oss_src.tgz
-- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb43_20140724oss
+- URL https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160526oss_src_0.tgz
+- DOWNLOAD_COMMAND curl -k -L https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160526oss_src_0.tgz -o tbb_20160526oss_src.tgz &&
+- tar -xzvf tbb_20160526oss_src.tgz
+- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb44_20160526oss
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- PATCH_COMMAND "${TBB_PATCH_STEP}"
- CONFIGURE_COMMAND ""
-- BUILD_COMMAND make CXXFLAGS=${TBB_CXXFLAGS} lambdas=1 compiler=${TBB_COMPILER} cfg=release tbb_build_prefix=LIBS
+- BUILD_COMMAND make CXXFLAGS=${TBB_CXXFLAGS} lambdas=1 compiler=${TBB_COMPILER} cfg=release tbb_build_prefix=LIBS
- INSTALL_COMMAND sh -c "cp ${TBB_SOURCE_DIR}/build/LIBS_release/*.${SHARED_LIB_EXTENSION}* ${TBB_INSTALL_DIR}/lib && cp -r ${TBB_SOURCE_DIR}/include/* ${TBB_INSTALL_DIR}/include"
- BUILD_IN_SOURCE 1
-)
-+ # set(TBB_CXXFLAGS "${TBB_CXXFLAGS} -UDO_ITT_NOTIFY")
+#endif()
-SET( RECONFIG_FLAGS ${RECONFIG_FLAGS} -DTBB_WILL_RECONFIGURE=FALSE -DTBB_RECONFIGURE=TRUE)
@@ -183,14 +190,14 @@ Description: Use Debian version of dependencies, don't download them
-endif()
+#ExternalProject_Add(libtbb
+# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-+# URL http://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb43_20140724oss_src.tgz
-+# DOWNLOAD_COMMAND curl -k -L http://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb43_20140724oss_src.tgz -o tbb_20140724oss_src.tgz &&
-+# tar -xzvf tbb_20140724oss_src.tgz
-+# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb43_20140724oss
++# URL https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160526oss_src_0.tgz
++# DOWNLOAD_COMMAND curl -k -L https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160526oss_src_0.tgz -o tbb_20160526oss_src.tgz &&
++# tar -xzvf tbb_20160526oss_src.tgz
++# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb44_20160526oss
+# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+# PATCH_COMMAND "${TBB_PATCH_STEP}"
+# CONFIGURE_COMMAND ""
-+# BUILD_COMMAND make CXXFLAGS=${TBB_CXXFLAGS} lambdas=1 compiler=${TBB_COMPILER} cfg=release tbb_build_prefix=LIBS
++# BUILD_COMMAND make CXXFLAGS=${TBB_CXXFLAGS} lambdas=1 compiler=${TBB_COMPILER} cfg=release tbb_build_prefix=LIBS
+# 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
+#)
@@ -254,17 +261,40 @@ Description: Use Debian version of dependencies, don't download them
-message("==================================================================")
-ExternalProject_Add(libgff
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- URL http://www.cs.cmu.edu/~robp/files/libgff.tgz
+- DOWNLOAD_COMMAND curl -k -L https://github.com/Kingsford-Group/libgff/archive/v1.0.tar.gz -o libgff.tgz &&
+- tar -xzvf libgff.tgz &&
+- rm -fr libgff &&
+- mv libgff-1.0 libgff
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libgff
- UPDATE_COMMAND sh -c "mkdir -p <SOURCE_DIR>/build"
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- BINARY_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libgff/build
- CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_CURRENT_SOURCE_DIR}/external/install
-)
--
++#message("Build system will compile libgff")
++#message("==================================================================")
++#ExternalProject_Add(libgff
++# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
++# DOWNLOAD_COMMAND curl -k -L https://github.com/Kingsford-Group/libgff/archive/v1.0.tar.gz -o libgff.tgz &&
++# tar -xzvf libgff.tgz &&
++# rm -fr libgff &&
++# mv libgff-1.0 libgff
++# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libgff
++# UPDATE_COMMAND sh -c "mkdir -p <SOURCE_DIR>/build"
++# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
++# BINARY_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libgff/build
++# CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_CURRENT_SOURCE_DIR}/external/install
++#)
+
+ # Because of the way that Apple has changed SIP
+ # in el capitan, some headers may be in a new location
+@@ -502,39 +502,39 @@ if (APPLE)
+ endif()
+
+
-message("Build system will compile Staden IOLib")
-message("==================================================================")
--ExternalProject_Add(libstadenio
+-ExternalProject_Add(libstadenio
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/staden-io_lib/releases/download/v1.13.10/io_lib-1.13.10.tar.gz -o staden-io_lib-v1.13.10.tar.gz &&
- mkdir -p staden-io_lib-1.13.10 &&
@@ -274,7 +304,8 @@ Description: Use Debian version of dependencies, don't download them
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/staden-io_lib
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- CONFIGURE_COMMAND ./configure --enable-shared=no --without-libcurl --prefix=<INSTALL_DIR> LDFLAGS=${LIBSTADEN_LDFLAGS} CFLAGS=${LIBSTADEN_CFLAGS} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
-- BUILD_COMMAND make CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
+- BUILD_COMMAND make CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CFLAGS+=${STADEN_INC} CFLAGS+=${STADEN_LIB}
+-
- BUILD_IN_SOURCE 1
- INSTALL_COMMAND make install
-)
@@ -283,10 +314,10 @@ Description: Use Debian version of dependencies, don't download them
-message("==================================================================")
-ExternalProject_Add(libspdlog
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/spdlog/archive/v1.5.tar.gz -o spdlog-v1.5.tar.gz &&
-- tar -xzf spdlog-v1.5.tar.gz &&
+- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/spdlog/archive/v1.0.1.tar.gz -o spdlog-v1.0.1.tar.gz &&
+- tar -xzf spdlog-v1.0.1.tar.gz &&
- rm -fr spdlog &&
-- mv -f spdlog-1.5 spdlog
+- mv -f spdlog-1.0.1 spdlog
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/spdlog
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- CONFIGURE_COMMAND ""
@@ -294,21 +325,9 @@ Description: Use Debian version of dependencies, don't download them
- BUILD_IN_SOURCE 1
- INSTALL_COMMAND cp -r <SOURCE_DIR>/include/spdlog <INSTALL_DIR>/include
-)
-+#message("Build system will compile libgff")
-+#message("==================================================================")
-+#ExternalProject_Add(libgff
-+# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-+# URL http://www.cs.cmu.edu/~robp/files/libgff.tgz
-+# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libgff
-+# UPDATE_COMMAND sh -c "mkdir -p <SOURCE_DIR>/build"
-+# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-+# BINARY_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libgff/build
-+# CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_CURRENT_SOURCE_DIR}/external/install
-+#)
-+
+#message("Build system will compile Staden IOLib")
+#message("==================================================================")
-+#ExternalProject_Add(libstadenio
++#ExternalProject_Add(libstadenio
+# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+# DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/staden-io_lib/releases/download/v1.13.10/io_lib-1.13.10.tar.gz -o staden-io_lib-v1.13.10.tar.gz &&
+# mkdir -p staden-io_lib-1.13.10 &&
@@ -318,7 +337,8 @@ Description: Use Debian version of dependencies, don't download them
+# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/staden-io_lib
+# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+# CONFIGURE_COMMAND ./configure --enable-shared=no --without-libcurl --prefix=<INSTALL_DIR> LDFLAGS=${LIBSTADEN_LDFLAGS} CFLAGS=${LIBSTADEN_CFLAGS} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
-+# BUILD_COMMAND make CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
++# BUILD_COMMAND make CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CFLAGS+=${STADEN_INC} CFLAGS+=${STADEN_LIB}
++#
+# BUILD_IN_SOURCE 1
+# INSTALL_COMMAND make install
+#)
@@ -327,10 +347,10 @@ Description: Use Debian version of dependencies, don't download them
+#message("==================================================================")
+#ExternalProject_Add(libspdlog
+# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-+# DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/spdlog/archive/v1.5.tar.gz -o spdlog-v1.5.tar.gz &&
-+# tar -xzf spdlog-v1.5.tar.gz &&
++# DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/spdlog/archive/v1.0.1.tar.gz -o spdlog-v1.0.1.tar.gz &&
++# tar -xzf spdlog-v1.0.1.tar.gz &&
+# rm -fr spdlog &&
-+# mv -f spdlog-1.5 spdlog
++# mv -f spdlog-1.0.1 spdlog
+# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/spdlog
+# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+# CONFIGURE_COMMAND ""
@@ -341,7 +361,7 @@ Description: Use Debian version of dependencies, don't download them
set (FAST_MALLOC_LIB "")
set (HAVE_FAST_MALLOC FALSE)
-@@ -516,23 +518,23 @@
+@@ -558,23 +558,23 @@ if (NOT HAVE_FAST_MALLOC)
endif()
endif()
@@ -350,9 +370,9 @@ Description: Use Debian version of dependencies, don't download them
- message("==================================================================")
- ExternalProject_Add(libjemalloc
- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/jemalloc/archive/3.6.0.tar.gz -o jemalloc-3.6.0.tar.gz &&
-- tar -xzf jemalloc-3.6.0.tar.gz
-- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jemalloc-3.6.0
+- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/jemalloc/archive/4.0.4.tar.gz -o jemalloc-4.0.4.tar.gz &&
+- tar -xzf jemalloc-4.0.4.tar.gz
+- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jemalloc-4.0.4
- BUILD_IN_SOURCE TRUE
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- CONFIGURE_COMMAND sh -c "CC=${CMAKE_C_COMPILER} ./autogen.sh --prefix=<INSTALL_DIR>"
@@ -367,9 +387,9 @@ Description: Use Debian version of dependencies, don't download them
+# message("==================================================================")
+# ExternalProject_Add(libjemalloc
+# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-+# DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/jemalloc/archive/3.6.0.tar.gz -o jemalloc-3.6.0.tar.gz &&
-+# tar -xzf jemalloc-3.6.0.tar.gz
-+# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jemalloc-3.6.0
++# DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/jemalloc/archive/4.0.4.tar.gz -o jemalloc-4.0.4.tar.gz &&
++# tar -xzf jemalloc-4.0.4.tar.gz
++# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jemalloc-4.0.4
+# BUILD_IN_SOURCE TRUE
+# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+# CONFIGURE_COMMAND sh -c "CC=${CMAKE_C_COMPILER} ./autogen.sh --prefix=<INSTALL_DIR>"
@@ -380,27 +400,26 @@ Description: Use Debian version of dependencies, don't download them
+# set (HAVE_FAST_MALLOC TRUE)
+#endif ()
- ###
- #
---- salmon.orig/src/CMakeLists.txt
-+++ salmon/src/CMakeLists.txt
-@@ -38,12 +38,8 @@
- include_directories(
+ ##
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -1,11 +1,7 @@
+ include_directories(
${GAT_SOURCE_DIR}/include
-${GAT_SOURCE_DIR}/include/eigen3
-${GAT_SOURCE_DIR}/external
-${GAT_SOURCE_DIR}/external/cereal/include
-${GAT_SOURCE_DIR}/external/install/include
--${GAT_SOURCE_DIR}/external/install/include/jellyfish-2.1.3
+-${GAT_SOURCE_DIR}/external/install/include/jellyfish-2.2.6
-${GAT_SOURCE_DIR}/external/install/include/bwa
+/usr/include/eigen3
+/usr/include/bwa
${ZLIB_INCLUDE_DIR}
${TBB_INCLUDE_DIRS}
${Boost_INCLUDE_DIRS}
-@@ -74,7 +70,7 @@
- set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
+@@ -107,7 +103,7 @@ else()
+ endif()
# Build the Salmon library
-add_library(salmon_core STATIC ${SALMON_LIB_SRCS} )
@@ -408,16 +427,18 @@ Description: Use Debian version of dependencies, don't download them
# Build the salmon executable
add_executable(salmon ${SALMON_MAIN_SRCS} ${SALMON_ALIGN_SRCS})
-@@ -107,10 +103,10 @@
+@@ -131,12 +127,12 @@ target_link_libraries(salmon
gff
${PTHREAD_LIB}
- ${Boost_LIBRARIES}
+ ${Boost_LIBRARIES}
- ${GAT_SOURCE_DIR}/external/install/lib/libstaden-read.a
+ libstaden-read.so
- ${ZLIB_LIBRARY}
-- ${GAT_SOURCE_DIR}/external/install/lib/libjellyfish-2.0.a
+ ${ZLIB_LIBRARY}
+ ${SUFFARRAY_LIB}
+ ${SUFFARRAY64_LIB}
+- ${GAT_SOURCE_DIR}/external/install/lib/libjellyfish-2.0.a
- ${GAT_SOURCE_DIR}/external/install/lib/libbwa.a
-+ libjellyfish-2.0.so
++ libjellyfish-2.0.so
+ /usr/lib/libbwa.a
m
${LIBLZMA_LIBRARIES}
diff --git a/debian/patches/disable-version-check b/debian/patches/disable-version-check
index 3cb4e53..0c3eb70 100644
--- a/debian/patches/disable-version-check
+++ b/debian/patches/disable-version-check
@@ -1,8 +1,8 @@
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Description: Disable the newer version check
---- salmon.orig/src/Salmon.cpp
-+++ salmon/src/Salmon.cpp
-@@ -159,10 +159,10 @@
+--- a/src/Salmon.cpp
++++ b/src/Salmon.cpp
+@@ -181,10 +181,10 @@ int main( int argc, char* argv[] ) {
std::exit(0);
}
@@ -14,6 +14,6 @@ Description: Disable the newer version check
+ // std::string versionMessage = getVersionMessage();
+ // std::cerr << versionMessage;
+ //}
-
+
po::notify(vm);
diff --git a/debian/patches/drop-mathjax b/debian/patches/drop-mathjax
deleted file mode 100644
index b3fee22..0000000
--- a/debian/patches/drop-mathjax
+++ /dev/null
@@ -1,12 +0,0 @@
-Author: Michael R. Crusoe
-Description: Drop unused dependency on mathjax
---- salmon.orig/doc/source/conf.py
-+++ salmon/doc/source/conf.py
-@@ -31,7 +31,6 @@
- extensions = [
- 'sphinx.ext.autodoc',
- 'sphinx.ext.todo',
-- 'sphinx.ext.mathjax',
- 'sphinx.ext.ifconfig',
- ]
-
diff --git a/debian/patches/jellyfish-update b/debian/patches/jellyfish-update
deleted file mode 100644
index dcc02f4..0000000
--- a/debian/patches/jellyfish-update
+++ /dev/null
@@ -1,106 +0,0 @@
-Author: Michael R. Crusoe
-Description: There is a newer version of libjellyfish in Debian, update to
-match.
---- salmon.orig/src/merge_files.cc
-+++ salmon/src/merge_files.cc
-@@ -29,6 +29,8 @@
- #include <jellyfish/rectangular_binary_matrix.hpp>
- #include <jellyfish/cpp_array.hpp>
-
-+namespace err = jellyfish::err;
-+
- using jellyfish::file_header;
- using jellyfish::RectangularBinaryMatrix;
- using jellyfish::mer_dna;
-@@ -96,7 +98,7 @@
- for(size_t i = 0; i < files.size(); i++) {
- files.init(i, input_files[i]);
- if(!files[i].is.good())
-- eraise(MergeError) << "Failed to open input file '" << input_files[i] << "'";
-+ throw MergeError(err::msg() << "Failed to open input file '" << input_files[i] << "'");
-
- file_header& h = files[i].header;
- if(i == 0) {
-@@ -115,22 +117,22 @@
- out_counter_len = std::min(out_counter_len, h.counter_len());
- } else {
- if(format != h.format())
-- eraise(MergeError) << "Can't merge files with different formats (" << format << ", " << h.format() << ")";
-+ throw MergeError(err::msg() << "Can't merge files with different formats (" << format << ", " << h.format() << ")");
- if(h.key_len() != key_len)
-- eraise(MergeError) << "Can't merge hashes of different key lengths (" << key_len << ", " << h.key_len() << ")";
-+ throw MergeError(err::msg() << "Can't merge hashes of different key lengths (" << key_len << ", " << h.key_len() << ")");
- if(h.max_reprobe_offset() != max_reprobe_offset)
-- eraise(MergeError) << "Can't merge hashes with different reprobing strategies";
-+ throw MergeError(err::msg() << "Can't merge hashes with different reprobing strategies");
- if(h.size() != size)
-- eraise(MergeError) << "Can't merge hash with different size (" << size << ", " << h.size() << ")";
-+ throw MergeError(err::msg() << "Can't merge hash with different size (" << size << ", " << h.size() << ")");
- if(h.matrix() != *matrix)
-- eraise(MergeError) << "Can't merge hash with different hash function";
-+ throw MergeError(err::msg() << "Can't merge hash with different hash function");
- }
- }
- mer_dna::k(key_len / 2);
-
- std::ofstream out(out_file);
- if(!out.good())
-- eraise(MergeError) << "Can't open out file '" << out_file << "'";
-+ throw MergeError(err::msg() << "Can't open out file '" << out_file << "'");
- out_header.format(format);
-
- if(!format.compare(binary_dumper::format)) {
-@@ -143,7 +145,7 @@
- text_writer writer;
- do_merge<text_reader, text_writer>(files, out, writer, min, max);
- } else {
-- eraise(MergeError) << "Unknown format '" << format << "'";
-+ throw MergeError(err::msg() << "Unknown format '" << format << "'");
- }
- out.close();
- }
---- salmon.orig/src/BuildSalmonIndex.cpp
-+++ salmon/src/BuildSalmonIndex.cpp
-@@ -21,7 +21,6 @@
- #include "cereal/types/vector.hpp"
- #include "cereal/archives/binary.hpp"
-
--#include "jellyfish/config.h"
- #include "jellyfish/err.hpp"
- #include "jellyfish/misc.hpp"
- #include "jellyfish/jellyfish.hpp"
---- salmon.orig/include/PairSequenceParser.hpp
-+++ salmon/include/PairSequenceParser.hpp
-@@ -130,9 +130,9 @@
- if(type1 == DONE_TYPE || type2 == DONE_TYPE)
- return open_next_files(st);
- if(type1 != type2)
-- eraise(std::runtime_error) << "Paired files are of different format";
-+ throw std::runtime_error("Paired files are of different format");
- if(type1 == ERROR_TYPE || type2 == ERROR_TYPE)
-- eraise(std::runtime_error) << "Unsupported format";
-+ throw std::runtime_error("Unsupported format");
- st.type = type1;
- }
-
-@@ -165,7 +165,7 @@
- hsq.seq.append(tmp); // two lines avoiding copying
- }
- if(!is.good())
-- eraise(std::runtime_error) << "Truncated fastq file";
-+ throw std::runtime_error("Truncated fastq file");
- is.ignore(std::numeric_limits<std::streamsize>::max(), '\n');
- hsq.qual.clear();
- while(hsq.qual.size() < hsq.seq.size() && is.good()) {
-@@ -173,9 +173,9 @@
- hsq.qual.append(tmp);
- }
- if(hsq.qual.size() != hsq.seq.size())
-- eraise(std::runtime_error) << "Invalid fastq file: wrong number of quals";
-+ throw std::runtime_error("Invalid fastq file: wrong number of quals");
- if(is.peek() != EOF && is.peek() != '@')
-- eraise(std::runtime_error) << "Invalid fastq file: header missing";
-+ throw std::runtime_error("Invalid fastq file: header missing");
-
- }
-
diff --git a/debian/patches/reproducible-build b/debian/patches/reproducible-build
deleted file mode 100644
index 265ccd6..0000000
--- a/debian/patches/reproducible-build
+++ /dev/null
@@ -1,22 +0,0 @@
-Author: Chris Lamb <lamby at debian.org>
-Description: makes the build reproducible
-Forwarded: https://github.com/COMBINE-lab/salmon/pull/40
---- salmon-0.4.2+ds1.orig/src/BuildSalmonIndex.cpp
-+++ salmon-0.4.2+ds1/src/BuildSalmonIndex.cpp
-@@ -151,7 +151,6 @@ int salmonIndex(int argc, char* argv[])
- bool useStreamingParser = true;
-
- uint32_t saSampInterval = 1;
-- uint32_t maxThreads = std::thread::hardware_concurrency();
- uint32_t numThreads;
-
- po::options_description generic("Command Line Options");
-@@ -160,7 +159,7 @@ int salmonIndex(int argc, char* argv[])
- ("help,h", "produce help message")
- ("transcripts,t", po::value<string>()->required(), "Transcript fasta file.")
- ("index,i", po::value<string>()->required(), "Salmon index.")
-- ("threads,p", po::value<uint32_t>(&numThreads)->default_value(maxThreads)->required(),
-+ ("threads,p", po::value<uint32_t>(&numThreads)->default_value(2)->required(),
- "Number of threads to use (only used for computing bias features)")
- ("sasamp,s", po::value<uint32_t>(&saSampInterval)->default_value(1)->required(),
- "The interval at which the suffix array should be sampled. "
diff --git a/debian/patches/series b/debian/patches/series
index c4872e9..fb2afc8 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,12 +1,7 @@
dependency-fix
-jellyfish-update
-cmake-adj
-drop-mathjax
cmake-typo-fixes
disable-version-check
use-system-pkg-config-tbb
0007-Remove-unnecessarily-linked-libraries.patch
0008-Remove-salmon_core-lib.patch
0009-Remove-FIND_PACKAGE-for-liblzma-and-libbz2.patch
-reproducible-build
-add_MEM_F_SELF_OVLP.patch
diff --git a/debian/patches/use-system-pkg-config-tbb b/debian/patches/use-system-pkg-config-tbb
index c272275..0abb43c 100644
--- a/debian/patches/use-system-pkg-config-tbb
+++ b/debian/patches/use-system-pkg-config-tbb
@@ -1,8 +1,8 @@
Description: Use pkgconfig to find the system library for tbb
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
---- salmon.orig/CMakeLists.txt
-+++ salmon/CMakeLists.txt
-@@ -169,6 +169,9 @@
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -180,6 +180,9 @@ set (Boost_USE_STATIC_LIBS OFF)
set (Boost_USE_MULTITHREADED ON)
#set (Boost_USE_STATIC_RUNTIME OFF)
@@ -12,9 +12,9 @@ Author: Michael R. Crusoe <crusoe at ucdavis.edu>
find_package (ZLIB)
if (NOT ZLIB_FOUND)
message (FATAL_ERROR "zlib must be installed before configuration & building can proceed")
-@@ -370,7 +373,8 @@
- # cp config.h <INSTALL_DIR>/include/
+@@ -398,7 +401,8 @@ set(SUFFARRAY_INCLUDE_DIRS ${CMAKE_CURRE
#)
+ #endif()
-find_package(TBB)
+#find_package(TBB)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index f31a927..ee1b87a 100755
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1,11 +1,7 @@
include_directories(
${GAT_SOURCE_DIR}/include
-${GAT_SOURCE_DIR}/include/eigen3
-${GAT_SOURCE_DIR}/external
-${GAT_SOURCE_DIR}/external/cereal/include
-${GAT_SOURCE_DIR}/external/install/include
-${GAT_SOURCE_DIR}/external/install/include/jellyfish-2.2.6
-${GAT_SOURCE_DIR}/external/install/include/bwa
+/usr/include/eigen3
+/usr/include/bwa
${ZLIB_INCLUDE_DIR}
${TBB_INCLUDE_DIRS}
${Boost_INCLUDE_DIRS}
@@ -107,7 +103,7 @@ else()
endif()
# Build the Salmon library
-add_library(salmon_core STATIC ${SALMON_LIB_SRCS} )
+add_library(salmon_core ${SALMON_LIB_SRCS} )
# Build the salmon executable
add_executable(salmon ${SALMON_MAIN_SRCS} ${SALMON_ALIGN_SRCS})
@@ -131,23 +127,19 @@ target_link_libraries(salmon
gff
${PTHREAD_LIB}
${Boost_LIBRARIES}
- ${GAT_SOURCE_DIR}/external/install/lib/libstaden-read.a
+ libstaden-read.so
${ZLIB_LIBRARY}
${SUFFARRAY_LIB}
${SUFFARRAY64_LIB}
- ${GAT_SOURCE_DIR}/external/install/lib/libjellyfish-2.0.a
- ${GAT_SOURCE_DIR}/external/install/lib/libbwa.a
+ libjellyfish-2.0.so
+ /usr/lib/libbwa.a
m
- ${LIBLZMA_LIBRARIES}
- ${BZIP2_LIBRARIES}
- ${TBB_LIBRARIES}
+ tbb
${LIBSALMON_LINKER_FLAGS}
${NON_APPLECLANG_LIBS}
${FAST_MALLOC_LIB}
)
-add_dependencies(salmon libbwa)
-
# Link the executable
target_link_libraries(unitTests
salmon_core
diff --git a/src/Salmon.cpp b/src/Salmon.cpp
index ffaf8c2..1f11b9b 100644
--- a/src/Salmon.cpp
+++ b/src/Salmon.cpp
@@ -181,10 +181,10 @@ int main( int argc, char* argv[] ) {
std::exit(0);
}
- if (!vm.count("no-version-check")){
- std::string versionMessage = getVersionMessage();
- std::cerr << versionMessage;
- }
+ //if (!vm.count("no-version-check")){
+ // std::string versionMessage = getVersionMessage();
+ // std::cerr << versionMessage;
+ //}
po::notify(vm);
diff --git a/src/SalmonQuantify.cpp b/src/SalmonQuantify.cpp
index c88940e..be14e92 100644
--- a/src/SalmonQuantify.cpp
+++ b/src/SalmonQuantify.cpp
@@ -1985,7 +1985,7 @@ int salmonQuantify(int argc, char* argv[]) {
(
"maxOcc,m",
po::value<int>(&(memOptions->max_occ))->default_value(200),
- "(S)MEMs occuring more than this many times won't be considered.")
+ "(S)MEMs occurring more than this many times won't be considered.")
(
"initUniform", po::bool_switch(&(sopt.initUniform))->default_value(false),
"initialize the offline inference with uniform parameters, rather than seeding with online parameters.")
--
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