[med-svn] [Git][med-team/salmon][master] Take over patches from previous version if applicable. Keep some for documentation purpose
Andreas Tille
gitlab at salsa.debian.org
Thu Dec 13 17:20:19 GMT 2018
Andreas Tille pushed to branch master at Debian Med / salmon
Commits:
eea6c1a3 by Andreas Tille at 2018-12-13T15:30:33Z
Take over patches from previous version if applicable. Keep some for documentation purpose
- - - - -
6 changed files:
- + debian/patches/0008-Remove-salmon_core-lib.patch
- + debian/patches/add_MEM_F_SELF_OVLP.patch
- + debian/patches/disable-version-check.patch
- debian/patches/series
- + debian/patches/use-system-pkg-config-tbb.patch
- debian/rules
Changes:
=====================================
debian/patches/0008-Remove-salmon_core-lib.patch
=====================================
@@ -0,0 +1,95 @@
+From: Kevin Murray <spam at kdmurray.id.au>
+Date: Sat, 30 Jan 2016 18:06:52 +0200
+Subject: Remove salmon_core lib
+Remark: This patch is deactivated
+ Upstream code has changed a lot and it is not documented why
+ salmon_core lib was removed. Before breaking anything the
+ hopefully harmles lib is created as upstream seems to consider
+ sensible.
+
+---
+ src/CMakeLists.txt | 8 ++------
+ 1 file changed, 2 insertions(+), 6 deletions(-)
+
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -102,9 +102,6 @@
+ 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})
+@@ -124,7 +121,6 @@
+
+ # Link the executable
+ target_link_libraries(salmon
+- salmon_core
+ gff
+ ${PTHREAD_LIB}
+ ${Boost_LIBRARIES}
+@@ -146,42 +142,41 @@
+ # External dependencies of salmon_core and salmon
+ ##
+ if (${FETCHED_JEMALLOC})
+- add_dependencies(salmon_core libjemalloc)
++ # add_dependencies(salmon_core libjemalloc)
+ add_dependencies(salmon libjemalloc)
+ endif()
+
+ if (${FETCHED_BOOST})
+- add_dependencies(salmon_core libboost)
++ # add_dependencies(salmon_core libboost)
+ add_dependencies(salmon libboost)
+ endif()
+
+ if (${FETCHED_JELLYFISH})
+- add_dependencies(salmon_core libjellyfish)
++ #add_dependencies(salmon_core libjellyfish)
+ add_dependencies(salmon libjellyfish)
+ endif()
+
+ if (${FETCHED_TBB})
+- add_dependencies(salmon_core libtbb)
++ #add_dependencies(salmon_core libtbb)
+ add_dependencies(salmon libtbb)
+ endif()
+
+-add_dependencies(salmon_core libcereal)
++#add_dependencies(salmon_core libcereal)
+ add_dependencies(salmon libcereal)
+-add_dependencies(salmon_core libstadenio)
++#add_dependencies(salmon_core libstadenio)
+ add_dependencies(salmon libstadenio)
+-add_dependencies(salmon_core libspdlog)
++#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_core libbwa)
+ add_dependencies(salmon libbwa)
+-add_dependencies(salmon_core libgff)
++#add_dependencies(salmon_core libgff)
+ add_dependencies(salmon libgff)
+-add_dependencies(salmon_core libdivsufsort)
++#add_dependencies(salmon_core libdivsufsort)
+ add_dependencies(salmon libdivsufsort)
+
+ # Link the executable
+ target_link_libraries(unitTests
+- salmon_core
+ gff
+ ${PTHREAD_LIB}
+ ${Boost_LIBRARIES}
+@@ -259,7 +254,7 @@
+ # install(FILES ${Boost_LIBRARIES}
+ # DESTINATION ${INSTALL_LIB_DIR})
+
+-install(TARGETS salmon salmon_core
++install(TARGETS salmon
+ RUNTIME DESTINATION bin
+ LIBRARY DESTINATION lib
+ ARCHIVE DESTINATION lib
=====================================
debian/patches/add_MEM_F_SELF_OVLP.patch
=====================================
@@ -0,0 +1,25 @@
+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.
+Remark: This patch is deactivated since current source code
+ builds nicely without it.
+Author: Sascha Steinbiss <sascha at steinbiss.name>
+--- a/src/SalmonQuantify.cpp
++++ b/src/SalmonQuantify.cpp
+@@ -54,6 +54,7 @@ extern "C" {
+ #include "ksort.h"
+ #include "kvec.h"
+ #include "utils.h"
++#define MEM_F_SELF_OVLP 0x40
+ }
+
+ // Jellyfish 2 include
+@@ -126,6 +127,7 @@ extern "C" {
+ #include "RapMapUtils.hpp"
+ //#include "TextBootstrapWriter.hpp"
+
++
+ /****** QUASI MAPPING DECLARATIONS *********/
+ using MateStatus = rapmap::utils::MateStatus;
+ using QuasiAlignment = rapmap::utils::QuasiAlignment;
=====================================
debian/patches/disable-version-check.patch
=====================================
@@ -0,0 +1,19 @@
+Author: Michael R. Crusoe <crusoe at ucdavis.edu>
+Description: Disable the newer version check
+--- a/src/Salmon.cpp
++++ b/src/Salmon.cpp
+@@ -208,10 +208,10 @@ int main(int argc, char* argv[]) {
+ std::exit(0);
+ }
+
+- if (!vm.count("no-version-check")) {
+- std::string versionMessage = getVersionMessage();
+- std::cout << versionMessage;
+- }
++ //if (!vm.count("no-version-check")) {
++ // std::string versionMessage = getVersionMessage();
++ // std::cout << versionMessage;
++ //}
+
+ // po::notify(vm);
+
=====================================
debian/patches/series
=====================================
@@ -1 +1,5 @@
use_debian_packaged_libs.patch
+disable-version-check.patch
+# use-system-pkg-config-tbb.patch
+# 0008-Remove-salmon_core-lib.patch
+# add_MEM_F_SELF_OVLP.patch
=====================================
debian/patches/use-system-pkg-config-tbb.patch
=====================================
@@ -0,0 +1,19 @@
+Description: Use pkgconfig to find the system library for tbb
+Remark: This patch is deactivated for the moment.
+ use_debian_packaged_libs.patch is able to detect tbb
+ and there is no point to fiddle around now any more.
+ However, may be this is more elegant and the patch is
+ left as documentation.
+Author: Michael R. Crusoe <crusoe at ucdavis.edu>
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -287,6 +287,9 @@ endif()
+ 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")
=====================================
debian/rules
=====================================
@@ -25,6 +25,9 @@ CMAKE_EXTRA_FLAGS += -DDEBIAN_BUILD=1 \
dh $@ --with sphinxdoc
override_dh_auto_configure:
+ # See here
+ # https://github.com/COMBINE-lab/salmon/issues/87
+ # for a discussion with upstream why it is necessary to include rapmap source
mkdir -p $(CURDIR)/external/install/src/rapmap
cp -av /usr/share/rapmap/src/* $(CURDIR)/external/install/src/rapmap
dh_auto_configure -- $(CMAKE_EXTRA_FLAGS)
View it on GitLab: https://salsa.debian.org/med-team/salmon/commit/eea6c1a38ffac3dd8dded8144582ff61ff6a587e
--
View it on GitLab: https://salsa.debian.org/med-team/salmon/commit/eea6c1a38ffac3dd8dded8144582ff61ff6a587e
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