[med-svn] [salmon] 03/07: Try hard to adapt all patches
Andreas Tille
tille at debian.org
Tue Jan 24 13:17:29 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository salmon.
commit a87ef14253c9525a0d5912aaaa4d6ca7ae73c527
Author: Andreas Tille <tille at debian.org>
Date: Tue Jan 24 14:05:53 2017 +0100
Try hard to adapt all patches
---
...007-Remove-unnecessarily-linked-libraries.patch | 39 +-
debian/patches/0008-Remove-salmon_core-lib.patch | 18 +-
...emove-FIND_PACKAGE-for-liblzma-and-libbz2.patch | 68 +---
debian/patches/add_MEM_F_SELF_OVLP.patch | 4 +-
debian/patches/cmake-typo-fixes | 2 +-
debian/patches/dependency-fix | 412 ++++++---------------
debian/patches/disable-version-check | 6 +-
debian/patches/fix-unittest.patch | 2 +-
debian/patches/reproducible.patch | 6 +-
debian/patches/use-system-pkg-config-tbb | 16 +-
debian/patches/use_debian_packaged_rapmap.patch | 23 +-
debian/rules | 2 +
12 files changed, 183 insertions(+), 415 deletions(-)
diff --git a/debian/patches/0007-Remove-unnecessarily-linked-libraries.patch b/debian/patches/0007-Remove-unnecessarily-linked-libraries.patch
index 1bf1677..1992028 100644
--- a/debian/patches/0007-Remove-unnecessarily-linked-libraries.patch
+++ b/debian/patches/0007-Remove-unnecessarily-linked-libraries.patch
@@ -7,9 +7,20 @@ Subject: Remove unnecessarily linked libraries
src/CMakeLists.txt | 6 +-----
2 files changed, 2 insertions(+), 6 deletions(-)
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -264,7 +264,7 @@ 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 1.61.0 COMPONENTS iostreams filesystem system thread timer chrono program_options)
++find_package(Boost 1.61.0 COMPONENTS iostreams filesystem system thread timer program_options)
+ message("BOOST_INCLUDEDIR = ${BOOST_INCLUDEDIR}")
+ message("BOOST_LIBRARYDIR = ${BOOST_LIBRARYDIR}")
+ message("Boost_FOUND = ${Boost_FOUND}")
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
-@@ -135,16 +135,12 @@
+@@ -135,9 +135,7 @@ target_link_libraries(salmon
jellyfish-2.0
bwa
m
@@ -20,21 +31,11 @@ Subject: Remove unnecessarily linked libraries
${LIBSALMON_LINKER_FLAGS}
${NON_APPLECLANG_LIBS}
${FAST_MALLOC_LIB}
- )
-
--add_dependencies(salmon libbwa)
--
- # Link the executable
- target_link_libraries(unitTests
- salmon_core
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -240,7 +240,7 @@
- # 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 1.61.0 COMPONENTS iostreams filesystem system thread timer chrono program_options serialization)
-+find_package(Boost 1.61.0 COMPONENTS iostreams filesystem system thread timer program_options)
- message("BOOST_INCLUDEDIR = ${BOOST_INCLUDEDIR}")
- message("BOOST_LIBRARYDIR = ${BOOST_LIBRARYDIR}")
- message("Boost_FOUND = ${Boost_FOUND}")
+@@ -173,6 +171,7 @@ add_dependencies(salmon_core libstadenio
+ add_dependencies(salmon libstadenio)
+ add_dependencies(salmon_core libspdlog)
+ add_dependencies(salmon libspdlog)
++## FIXME: This was commented in version 0.7.2 in a quilt patch
+ add_dependencies(salmon_core libbwa)
+ add_dependencies(salmon libbwa)
+ add_dependencies(salmon_core libgff)
diff --git a/debian/patches/0008-Remove-salmon_core-lib.patch b/debian/patches/0008-Remove-salmon_core-lib.patch
index 1bd87fd..8f59b1d 100644
--- a/debian/patches/0008-Remove-salmon_core-lib.patch
+++ b/debian/patches/0008-Remove-salmon_core-lib.patch
@@ -8,23 +8,17 @@ Subject: Remove salmon_core lib
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
-@@ -103,13 +103,10 @@
+@@ -102,9 +102,6 @@ else()
set(CMAKE_INSTALL_RPATH_USE_LINK_PATH FALSE)
endif()
-# Build the Salmon library
-add_library(salmon_core ${SALMON_LIB_SRCS} )
-
- # Build the salmon executable
--add_executable(salmon ${SALMON_MAIN_SRCS} ${SALMON_ALIGN_SRCS})
-+add_executable(salmon ${SALMON_LIB_SRCS} ${SALMON_MAIN_SRCS} ${SALMON_ALIGN_SRCS})
-
--add_executable(unitTests ${UNIT_TESTS_SRCS})
-+add_executable(unitTests ${SALMON_LIB_SRCS} ${UNIT_TESTS_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"
-@@ -124,7 +121,6 @@
+ # Build the salmon executable
+ add_executable(salmon ${SALMON_MAIN_SRCS} ${SALMON_ALIGN_SRCS})
+@@ -124,7 +121,6 @@ set (SUFFARRAY64_LIB ${GAT_SOURCE_DIR}/e
# Link the executable
target_link_libraries(salmon
@@ -32,7 +26,7 @@ Subject: Remove salmon_core lib
gff
${PTHREAD_LIB}
${Boost_LIBRARIES}
-@@ -143,7 +139,6 @@
+@@ -181,7 +177,6 @@ add_dependencies(salmon libdivsufsort)
# Link the executable
target_link_libraries(unitTests
@@ -40,7 +34,7 @@ Subject: Remove salmon_core lib
gff
${PTHREAD_LIB}
${Boost_LIBRARIES}
-@@ -218,7 +213,7 @@
+@@ -259,7 +254,7 @@ install(DIRECTORY
# install(FILES ${Boost_LIBRARIES}
# DESTINATION ${INSTALL_LIB_DIR})
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 a7b815c..05a7a4d 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
@@ -9,7 +9,7 @@ As these seem not to be required.
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-@@ -188,53 +188,53 @@
+@@ -209,57 +209,6 @@ if (NOT ZLIB_FOUND)
message (FATAL_ERROR "zlib must be installed before configuration & building can proceed")
endif()
@@ -24,40 +24,21 @@ As these seem not to be required.
- 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
+- BUILD_COMMAND make ${QUIET_MAKE}
+- INSTALL_COMMAND make ${QUIET_MAKE} install
-)
-+#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
+-
+-# 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")
+-set (FETCHED_LIBLZMA TRUE)
-else()
- 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")
@@ -69,39 +50,20 @@ As these seem not to be required.
- 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>
+- BUILD_COMMAND make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
+- INSTALL_COMMAND make ${QUIET_MAKE} install PREFIX=<INSTALL_DIR>
-)
-+#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
+-# 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")
+-set (FETCHED_LIBBZ2 TRUE)
-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: ${BZIP2_LIBRARIES}")
-+# message("===========================================")
-+#endif()
-
+-
##
# Set the latest version and look for what we need
+ ##
diff --git a/debian/patches/add_MEM_F_SELF_OVLP.patch b/debian/patches/add_MEM_F_SELF_OVLP.patch
index af72306..2eaa0b9 100644
--- a/debian/patches/add_MEM_F_SELF_OVLP.patch
+++ b/debian/patches/add_MEM_F_SELF_OVLP.patch
@@ -5,7 +5,7 @@ Description: redefine MEM_F_SELF_OVLP
Author: Sascha Steinbiss <sascha at steinbiss.name>
--- a/src/SalmonQuantify.cpp
+++ b/src/SalmonQuantify.cpp
-@@ -56,6 +56,7 @@
+@@ -54,6 +54,7 @@ extern "C" {
#include "ksort.h"
#include "kvec.h"
#include "utils.h"
@@ -13,7 +13,7 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
}
// Jellyfish 2 include
-@@ -128,6 +129,7 @@
+@@ -126,6 +127,7 @@ extern "C" {
#include "RapMapUtils.hpp"
//#include "TextBootstrapWriter.hpp"
diff --git a/debian/patches/cmake-typo-fixes b/debian/patches/cmake-typo-fixes
index 8dbd663..572c2da 100644
--- a/debian/patches/cmake-typo-fixes
+++ b/debian/patches/cmake-typo-fixes
@@ -2,7 +2,7 @@ Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Description: fix upstream's typos
--- a/src/SalmonQuantify.cpp
+++ b/src/SalmonQuantify.cpp
-@@ -2088,7 +2088,7 @@
+@@ -2277,7 +2277,7 @@ int salmonQuantify(int argc, char* argv[
(
"maxOcc,m",
po::value<int>(&(memOptions->max_occ))->default_value(200),
diff --git a/debian/patches/dependency-fix b/debian/patches/dependency-fix
index d85157b..00d19b5 100644
--- a/debian/patches/dependency-fix
+++ b/debian/patches/dependency-fix
@@ -2,34 +2,25 @@ Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Description: Use Debian version of dependencies, don't download them
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-@@ -23,7 +23,7 @@
- set (WARNING_IGNORE_FLAGS "-Wno-deprecated-register")
- set (BOOST_CXX_FLAGS "-Wno-deprecated-register -std=c++11")
+@@ -28,7 +28,7 @@ endif()
+
+ set (BOOST_CXX_FLAGS "${WARNING_IGNORE_FLAGS} -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
-@@ -176,7 +176,7 @@
- ##
- # 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)
-
-@@ -237,7 +237,7 @@
+@@ -261,7 +261,7 @@ 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 1.61.0 COMPONENTS iostreams filesystem system thread timer chrono program_options serialization)
+-find_package(Boost 1.53.0 COMPONENTS iostreams filesystem system thread timer chrono program_options)
++find_package(Boost 1.61.0 COMPONENTS iostreams filesystem system thread timer chrono program_options)
message("BOOST_INCLUDEDIR = ${BOOST_INCLUDEDIR}")
message("BOOST_LIBRARYDIR = ${BOOST_LIBRARYDIR}")
message("Boost_FOUND = ${Boost_FOUND}")
-@@ -333,70 +333,70 @@
+@@ -358,188 +358,17 @@ message("BOOST LIBRARIES = ${Boost_LIBRA
set(EXTERNAL_LIBRARY_PATH $CMAKE_CURRENT_SOURCE_DIR/lib)
@@ -41,12 +32,19 @@ Description: Use Debian version of dependencies, don't download them
- 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"
+- #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
-)
+-ExternalProject_Add_Step(libdivsufsort makedir
+- COMMAND mkdir -p <SOURCE_DIR>/build
+- COMMENT "Make build directory"
+- DEPENDEES download
+- DEPENDERS configure)
+-
-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)
@@ -56,12 +54,17 @@ Description: Use Debian version of dependencies, don't download them
- 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"
+- #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"
-)
+-ExternalProject_Add_Step(libcereal makedir
+- COMMAND mkdir -p <SOURCE_DIR>/build
+- COMMENT "Make build directory"
+- DEPENDEES download
+- DEPENDERS configure)
-
-message("Build system will fetch and build BWA (for Salmon)")
-message("==================================================================")
@@ -74,13 +77,13 @@ Description: Use Debian version of dependencies, don't download them
- 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}"
+- BUILD_COMMAND sh -c "make ${QUIET_MAKE} CC=${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)
--
+ find_package(Jellyfish 2.2.6)
+
-if (NOT JELLYFISH_FOUND)
-message("Build system will fetch and build Jellyfish")
-message("==================================================================")
@@ -94,86 +97,23 @@ Description: Use Debian version of dependencies, don't download them
- 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
+- INSTALL_COMMAND make ${QUIET_MAKE} install
-)
+-set (FETCHED_JELLYFISH TRUE)
-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)
-+#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)
-
-@@ -405,94 +405,94 @@
- # Fetch and build Intel's Threading Building Blocks library.
- #
- ##
--if(NOT TBB_FOUND)
-+#if(NOT TBB_FOUND)
+-
+ ## Try and find TBB first
+ find_package(TBB 4.4 COMPONENTS tbb tbbmalloc tbbmalloc_proxy )
+-##
+-#
+-# Fetch and build Intel's Threading Building Blocks library.
+-#
+-##
+-if((NOT TBB_FOUND) OR (TBB_FOUND AND (TBB_VERSION VERSION_LESS 4.4)))
+-
-set(TBB_WILL_RECONFIGURE TRUE)
-+#set(TBB_WILL_RECONFIGURE TRUE)
- # Set the appropriate compiler
+-# Set the appropriate compiler
-if (CLANG)
- set(TBB_COMPILER "clang")
-else()
@@ -183,38 +123,25 @@ 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/tbb44_20160526oss)
+-set(TBB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb-2017_U3)
-set(TBB_INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install)
-+#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 ("${TBB_COMPILER}" STREQUAL "gcc")
## Don't know why it's a problem yet, but if we're using
## GCC, get rid of the DO_ITT_NOTIFY flag
set(TBB_CXXFLAGS "${TBB_CXXFLAGS} -UDO_ITT_NOTIFY")
-endif()
-+#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
+- #URL https://github.com/01org/tbb/archive/2017_U3.tar.gz
+- DOWNLOAD_COMMAND curl -k -L https://github.com/01org/tbb/archive/2017_U3.tar.gz -o tbb-2017_U3.tgz &&
+- tar -xzvf tbb-2017_U3.tgz
+- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb-2017_U3
- 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 ${QUIET_MAKE} CXXFLAGS=${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
-)
@@ -224,32 +151,14 @@ Description: Use Debian version of dependencies, don't download them
- COMMAND ${CMAKE_COMMAND} ${CMAKE_CURRENT_SOURCE_DIR} ${RECONFIG_FLAGS}
- DEPENDEES install
-)
+-
+-set (FETCHED_TBB TRUE)
-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 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)
@@ -258,20 +167,12 @@ Description: Use Debian version of dependencies, don't download them
- ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib/libtbbmalloc.${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.
- ##
+-
+-##
+-# 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)
@@ -281,16 +182,7 @@ Description: Use Debian version of dependencies, don't download them
- 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}")
@@ -298,36 +190,28 @@ Description: Use Debian version of dependencies, don't download them
-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 &&
+- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -o libgff.tgz &&
- tar -xzvf libgff.tgz &&
- rm -fr libgff &&
-- mv libgff-1.0 libgff
+- mv libgff-1.1 libgff
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libgff
-- UPDATE_COMMAND sh -c "mkdir -p <SOURCE_DIR>/build"
+- #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
+-ExternalProject_Add_Step(libgff makedir
+- COMMAND mkdir -p <SOURCE_DIR>/build
+- COMMENT "Make build directory"
+- DEPENDEES download
+- DEPENDERS configure)
+-
+ # Because of the way that Apple has changed SIP
# in el capitan, some headers may be in a new location
-@@ -502,39 +502,39 @@
- endif()
-
+ if (APPLE)
+@@ -553,40 +382,6 @@ else ()
+ set(LZFLAG "")
+ endif (CONDA_BUILD)
-message("Build system will compile Staden IOLib")
-message("==================================================================")
@@ -341,7 +225,7 @@ 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=${CMAKE_CXX_COMPILER} CFLAGS+=${STADEN_INC} CFLAGS+=${STADEN_LIB}
+- BUILD_COMMAND make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CFLAGS+=${STADEN_INC} CFLAGS+=${STADEN_LIB} CFLAGS+=${LZFLAG}
-
- BUILD_IN_SOURCE 1
- INSTALL_COMMAND make install
@@ -351,10 +235,10 @@ 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/v1.12.tar.gz -o spdlog-v1.12.tar.gz &&
-- tar -xzf spdlog-v1.12.tar.gz &&
+- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/spdlog/archive/v0.11.0.tar.gz -o spdlog-v0.11.0.tar.gz &&
+- tar -xzf spdlog-v0.11.0.tar.gz &&
- rm -fr spdlog &&
-- mv -f spdlog-1.12 spdlog
+- mv -f spdlog-0.11.0 spdlog
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/spdlog
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- CONFIGURE_COMMAND ""
@@ -362,44 +246,12 @@ 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 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/archive/v1.14.8.tar.gz -o staden-io_lib-v1.14.8.tar.gz &&
-+# mkdir -p staden-io_lib-1.14.8 &&
-+# tar -xzf staden-io_lib-v1.14.8.tar.gz --strip-components=1 -C staden-io_lib-1.14.8 &&
-+# rm -fr staden-io_lib &&
-+# mv -f staden-io_lib-1.14.8 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/v1.12.tar.gz -o spdlog-v1.12.tar.gz &&
-+# tar -xzf spdlog-v1.12.tar.gz &&
-+# rm -fr spdlog &&
-+# mv -f spdlog-1.12 spdlog
-+# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/spdlog
-+# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-+# CONFIGURE_COMMAND ""
-+# BUILD_COMMAND ""
-+# BUILD_IN_SOURCE 1
-+# INSTALL_COMMAND cp -r <SOURCE_DIR>/include/spdlog <INSTALL_DIR>/include
-+#)
-
+-
set (FAST_MALLOC_LIB "")
set (HAVE_FAST_MALLOC FALSE)
-@@ -558,40 +558,40 @@
- endif()
+
+@@ -615,50 +410,6 @@ else ()
+ set (JEMALLOC_FLAGS "CC=${CMAKE_C_COMPILER}")
endif()
-if (NOT HAVE_FAST_MALLOC)
@@ -407,67 +259,48 @@ 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/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
+- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/jemalloc/archive/4.4.0.tar.gz -o jemalloc-4.4.0.tar.gz &&
+- tar -xzf jemalloc-4.4.0.tar.gz
+- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jemalloc-4.4.0
- 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>"
+- CONFIGURE_COMMAND sh -c "${JEMALLOC_FLAGS} ./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)
+- set (FETCHED_JEMALLOC TRUE)
+- if (FETCHED_LIBBZ2)
+- add_dependencies(libjemalloc libbz2)
+- endif()
+-
+- if (FETCHED_LIBLZMA)
+- add_dependencies(libjemalloc liblzma)
+- 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 ()
-
-
- ##
- ## 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
-+#)
-
+-
+-
+-##
+-## 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
+-#)
+-
###
#
+ # Done building external dependencies.
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1,11 +1,7 @@
@@ -484,7 +317,7 @@ Description: Use Debian version of dependencies, don't download them
${ZLIB_INCLUDE_DIR}
${TBB_INCLUDE_DIRS}
${Boost_INCLUDE_DIRS}
-@@ -71,6 +67,7 @@
+@@ -70,6 +66,7 @@ SGSmooth.cpp
set ( UNIT_TESTS_SRCS
${GAT_SOURCE_DIR}/tests/UnitTests.cpp
FragmentLengthDistribution.cpp
@@ -492,16 +325,16 @@ Description: Use Debian version of dependencies, don't download them
)
-@@ -107,7 +104,7 @@
+@@ -106,7 +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})
-@@ -131,12 +128,12 @@
+@@ -131,12 +128,12 @@ target_link_libraries(salmon
gff
${PTHREAD_LIB}
${Boost_LIBRARIES}
@@ -519,7 +352,7 @@ Description: Use Debian version of dependencies, don't download them
m
${LIBLZMA_LIBRARIES}
${BZIP2_LIBRARIES}
-@@ -154,12 +151,12 @@
+@@ -189,12 +186,12 @@ target_link_libraries(unitTests
gff
${PTHREAD_LIB}
${Boost_LIBRARIES}
@@ -537,12 +370,3 @@ Description: Use Debian version of dependencies, don't download them
m
${LIBLZMA_LIBRARIES}
${BZIP2_LIBRARIES}
-@@ -167,7 +164,7 @@
- ${LIBSALMON_LINKER_FLAGS}
- ${NON_APPLECLANG_LIBS}
- ${FAST_MALLOC_LIB}
-- )
-+)
-
- ### No need for this, I think
- ## This ensures that the salmon executable should work with or without `make install`
diff --git a/debian/patches/disable-version-check b/debian/patches/disable-version-check
index 6712c6b..bd48c5d 100644
--- a/debian/patches/disable-version-check
+++ b/debian/patches/disable-version-check
@@ -2,8 +2,8 @@ Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Description: Disable the newer version check
--- a/src/Salmon.cpp
+++ b/src/Salmon.cpp
-@@ -179,10 +179,10 @@
- std::exit(0);
+@@ -210,10 +210,10 @@ int main( int argc, char* argv[] ) {
+ std::exit(0);
}
- if (!vm.count("no-version-check")){
@@ -15,5 +15,5 @@ Description: Disable the newer version check
+ // std::cerr << versionMessage;
+ //}
- po::notify(vm);
+ //po::notify(vm);
diff --git a/debian/patches/fix-unittest.patch b/debian/patches/fix-unittest.patch
index 12d2d5c..c11599d 100644
--- a/debian/patches/fix-unittest.patch
+++ b/debian/patches/fix-unittest.patch
@@ -2,7 +2,7 @@ Description: fix path of unittest executable
Author: Sascha Steinbiss <satta at debian.org>
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
-@@ -237,7 +237,7 @@
+@@ -279,7 +279,7 @@ install(
)
include(InstallRequiredSystemLibraries)
diff --git a/debian/patches/reproducible.patch b/debian/patches/reproducible.patch
index 085c77d..61ad7a6 100644
--- a/debian/patches/reproducible.patch
+++ b/debian/patches/reproducible.patch
@@ -4,12 +4,12 @@ Description: make build reproducible
Author: Sascha Steinbiss <satta at debian.org>
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-@@ -27,7 +27,7 @@
+@@ -32,7 +32,7 @@ set (BOOST_CXX_FLAGS "${WARNING_IGNORE_F
## Set the standard required compile flags
# Nov 18th --- removed -DHAVE_CONFIG_H
--set (CMAKE_CXX_FLAGS "-pthread -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DRAPMAP_SALMON_SUPPORT -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -std=c++11 -Wreturn-type -Werror=return-type")
-+set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DRAPMAP_SALMON_SUPPORT -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -std=c++11 -Wreturn-type -Werror=return-type")
+-set (CMAKE_CXX_FLAGS "-pthread -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DRAPMAP_SALMON_SUPPORT -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -std=c++11 -Wreturn-type -Werror=return-type")
++set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DRAPMAP_SALMON_SUPPORT -DHAVE_ANSI_TERM -DHAVE_SSTREAM -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -std=c++11 -Wreturn-type -Werror=return-type")
##
# OSX is strange (some might say, stupid in this regard). Deal with it's quirkines here.
diff --git a/debian/patches/use-system-pkg-config-tbb b/debian/patches/use-system-pkg-config-tbb
index 0abb43c..0c99814 100644
--- a/debian/patches/use-system-pkg-config-tbb
+++ b/debian/patches/use-system-pkg-config-tbb
@@ -2,7 +2,7 @@ Description: Use pkgconfig to find the system library for tbb
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-@@ -180,6 +180,9 @@ set (Boost_USE_STATIC_LIBS OFF)
+@@ -201,6 +201,9 @@ endif(CONDA_BUILD)
set (Boost_USE_MULTITHREADED ON)
#set (Boost_USE_STATIC_RUNTIME OFF)
@@ -12,13 +12,11 @@ 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")
-@@ -398,7 +401,8 @@ set(SUFFARRAY_INCLUDE_DIRS ${CMAKE_CURRE
- #)
- #endif()
+@@ -361,6 +364,7 @@ set(EXTERNAL_LIBRARY_PATH $CMAKE_CURRENT
+ find_package(Jellyfish 2.2.6)
--find_package(TBB)
-+#find_package(TBB)
-+
+ ## Try and find TBB first
++## FIXME: This was commented in version 0.7.2 in a quilt patch
+ find_package(TBB 4.4 COMPONENTS tbb tbbmalloc tbbmalloc_proxy )
- ##
- #
+ ## Don't know why it's a problem yet, but if we're using
diff --git a/debian/patches/use_debian_packaged_rapmap.patch b/debian/patches/use_debian_packaged_rapmap.patch
index 60f8dd6..5f8fe20 100644
--- a/debian/patches/use_debian_packaged_rapmap.patch
+++ b/debian/patches/use_debian_packaged_rapmap.patch
@@ -5,7 +5,7 @@ Description: use debian packaged RapMap
Author: Sascha Steinbiss <satta at debian.org>
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
-@@ -5,7 +5,6 @@
+@@ -5,7 +5,6 @@ ${GAT_SOURCE_DIR}/include
${ZLIB_INCLUDE_DIR}
${TBB_INCLUDE_DIRS}
${Boost_INCLUDE_DIRS}
@@ -13,14 +13,13 @@ Author: Sascha Steinbiss <satta at debian.org>
)
if (JELLYFISH_FOUND)
-@@ -20,14 +19,6 @@
+@@ -20,13 +19,6 @@ is.c
bwt_gen.c
bwtindex.c
xxhash.c
-${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
--${GAT_SOURCE_DIR}/external/install/src/rapmap/RapMapSAMapper.cpp
-${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
@@ -28,7 +27,7 @@ Author: Sascha Steinbiss <satta at debian.org>
CollapsedEMOptimizer.cpp
CollapsedGibbsSampler.cpp
Salmon.cpp
-@@ -38,7 +29,6 @@
+@@ -37,7 +29,6 @@ FragmentStartPositionDistribution.cpp
SequenceBiasModel.cpp
TranscriptGroup.cpp
GZipWriter.cpp
@@ -36,7 +35,7 @@ Author: Sascha Steinbiss <satta at debian.org>
)
set (SALMON_ALIGN_SRCS
-@@ -64,6 +54,16 @@
+@@ -63,6 +54,16 @@ SimplePosBias.cpp
SGSmooth.cpp
)
@@ -53,21 +52,9 @@ Author: Sascha Steinbiss <satta at debian.org>
set ( UNIT_TESTS_SRCS
${GAT_SOURCE_DIR}/tests/UnitTests.cpp
FragmentLengthDistribution.cpp
-@@ -104,9 +104,9 @@
- endif()
-
- # Build the salmon executable
--add_executable(salmon ${SALMON_LIB_SRCS} ${SALMON_MAIN_SRCS} ${SALMON_ALIGN_SRCS})
-+add_executable(salmon ${SALMON_LIB_SRCS} ${SALMON_MAIN_SRCS} ${SALMON_ALIGN_SRCS} ${RAPMAP_EMBED_SRCS})
-
--add_executable(unitTests ${SALMON_LIB_SRCS} ${UNIT_TESTS_SRCS})
-+add_executable(unitTests ${SALMON_LIB_SRCS} ${UNIT_TESTS_SRCS} ${RAPMAP_EMBED_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"
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-@@ -161,7 +161,7 @@
+@@ -177,7 +177,7 @@ set (GAT_SOURCE_DIR ${CMAKE_CURRENT_SOUR
#
####
if(NOT FETCHED_RAPMAP)
diff --git a/debian/rules b/debian/rules
index 6d8ceb0..0497961 100755
--- a/debian/rules
+++ b/debian/rules
@@ -8,6 +8,8 @@ VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//'
# Fails to build when trying to enhance hardening
export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
+CMAKE_EXTRA_FLAGS += -DCONDA_BUILD=1
+
%:
dh $@ --with sphinxdoc --parallel
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/salmon.git
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