manta-relax-dependency-checking.patch

diff -urB manta-1.6.0-orig/CMakeLists.txt manta-1.6.0/CMakeLists.txt
--- a/CMakeLists.txt	2019-06-24 22:02:16.000000000 +0200
+++ b/CMakeLists.txt	2020-07-07 12:44:01.246483878 +0200
@@ -53,7 +53,7 @@
 #
 # if true, build with very strict error checking (disabled in src release tarballs)
 #
-set(DEVELOPER_MODE true)
+set(DEVELOPER_MODE false)
 
 #
 # set WIN specific cache values
@@ -205,7 +205,8 @@
 add_custom_target(${THIS_OPT} ALL)
 
 # redist includes
-include ("${THIS_MODULE_DIR}/boost.cmake")
+set(Boost_LIBRARIES "-lboost_chrono -lboost_date_time -lboost_filesystem -lboost_program_options -lboost_regex -lboost_serialization -lboost_system -lboost_timer -lboost_unit_test_framework")
+ADD_DEFINITIONS(-DBOOST_TEST_DYN_LINK)
 
 if (NOT WIN32)
     # global source QC -- don't allow non-ascii chars in source files:
diff -urB manta-1.6.0-orig/redist/CMakeLists.txt manta-1.6.0/redist/CMakeLists.txt
--- a/redist/CMakeLists.txt	2019-06-24 22:02:16.000000000 +0200
+++ b/redist/CMakeLists.txt	2020-07-07 11:21:43.665094771 +0200
@@ -71,87 +71,14 @@
 #
 # htslib
 #
-set(HTSLIB_PREFIX "htslib-1.9")
-superset(HTSLIB_DIR "${CMAKE_CURRENT_BINARY_DIR}/${HTSLIB_PREFIX}")
-superset(HTSLIB_LIBRARY "${HTSLIB_DIR}/libhts.a")
-
-## It is occasionally useful to extend debug/asan build options from manta all the way down through htslib,
-## the flags below can be uncommented to do so.
-##
-## Addresss sanitizer build options for htslib/samtools
-#set(HTSLIB_CFLAGS '-O0 -g -fsanitize=address -fno-omit-frame-pointer -fno-optimize-sibling-calls')
-## Debug build optoins for htslib/samtools
-#set(HTSLIB_CFLAGS '-O0 -g')
-#set(HTSLIB_CONFIGOPT CFLAGS=${HTSLIB_CFLAGS} LDFLAGS=${HTSLIB_CFLAGS})
-
-add_custom_command(
-    OUTPUT ${HTSLIB_DIR}
-    COMMAND ${CMAKE_COMMAND} -E remove_directory "${HTSLIB_DIR}"
-    COMMAND ${CMAKE_COMMAND} -E tar xjf "${THIS_REDIST_DIR}/${HTSLIB_PREFIX}.tar.bz2"
-    COMMENT "Unpacking htslib library")
-
-set (HTSLIB_FINAL_TASK ${HTSLIB_DIR})
-
-if (NOT WIN32)
-    add_custom_command(
-        OUTPUT ${HTSLIB_LIBRARY}
-        COMMAND ./configure CC=${CMAKE_C_COMPILER} ${HTSLIB_CONFIGOPT} --disable-libcurl --disable-bz2 --disable-lzma >htslib.config.log 2>htslib.config.error.log || \(echo "Failed to configure htslib, see ${HTSLIB_DIR}/htslib.config.error.log for details." && exit 1\)
-        COMMAND $(MAKE) lib-static bgzip htsfile tabix >htslib.build.log 2>htslib.build.error.log || \(echo "Failed to build htslib, see ${HTSLIB_DIR}/htslib.build.error.log for details." && exit 1\)
-        WORKING_DIRECTORY ${HTSLIB_DIR}
-        DEPENDS ${HTSLIB_DIR}
-        COMMENT "Building htslib library")
-
-    set (HTSLIB_FINAL_TASK ${HTSLIB_LIBRARY})
-endif ()
-
-set(THIS_HTSLIB "${THIS_PROJECT_NAME}_htslib")
-add_custom_target(${THIS_HTSLIB} DEPENDS "${HTSLIB_FINAL_TASK}")
-
-
-if (NOT WIN32)
-    install(PROGRAMS "${HTSLIB_DIR}/bgzip" DESTINATION "${THIS_LIBEXECDIR}")
-    install(PROGRAMS "${HTSLIB_DIR}/htsfile" DESTINATION "${THIS_LIBEXECDIR}")
-    install(PROGRAMS "${HTSLIB_DIR}/tabix" DESTINATION "${THIS_LIBEXECDIR}")
-endif ()
+superset(HTSLIB_LIBRARY "-fPIC -lhts")
 
 #
 # samtools
 #
-set(SAMTOOLS_PREFIX "samtools-1.9")
-set(SAMTOOLS_DIR "${CMAKE_CURRENT_BINARY_DIR}/${SAMTOOLS_PREFIX}")
-set(SAMTOOLS_LIBRARY "${SAMTOOLS_DIR}/libbam.a")
+set(SAMTOOLS_DIR "/usr/bin")
 superset(SAMTOOLS_PROG "${SAMTOOLS_DIR}/samtools")
 
-# final directory copy below would ideally be a soft-link, copy is for windows build
-add_custom_command(
-    OUTPUT ${SAMTOOLS_DIR}
-    COMMAND ${CMAKE_COMMAND} -E remove_directory "${SAMTOOLS_DIR}"
-    COMMAND ${CMAKE_COMMAND} -E tar xjf "${THIS_REDIST_DIR}/${SAMTOOLS_PREFIX}.tar.bz2"
-    DEPENDS ${HTSLIB_FINAL_TASK}
-    COMMENT "Unpacking samtools package")
-
-set (SAMTOOLS_FINAL_TASK ${SAMTOOLS_DIR})
-
-if (NOT WIN32)
-    add_custom_command(
-        OUTPUT ${SAMTOOLS_PROG}
-        COMMAND ./configure CC=${CMAKE_C_COMPILER} ${HTSLIB_CONFIGOPT} --without-curses --with-htslib=${HTSLIB_DIR} >samtools.config.log 2>samtools.config.error.log || \(echo "Failed to configure samtools, see ${SAMTOOLS_DIR}/samtools.config.error.log for details." && exit 1\)
-        COMMAND $(MAKE) all >samtools.build.log 2>samtools.build.error.log  || \(echo "Failed to build samtools, see ${SAMTOOLS_DIR}/samtools.build.error.log for details." && exit 1\)
-        DEPENDS ${HTSLIB_LIBRARY}
-        DEPENDS ${SAMTOOLS_DIR}
-        WORKING_DIRECTORY ${SAMTOOLS_DIR}
-        COMMENT "Building samtools package")
-
-    set (SAMTOOLS_FINAL_TASK ${SAMTOOLS_PROG})
-endif ()
-
-set(THIS_SAMTOOLS "${THIS_PROJECT_NAME}_samtools")
-add_custom_target(${THIS_SAMTOOLS} DEPENDS "${SAMTOOLS_FINAL_TASK}")
-
-if (NOT WIN32)
-    install(PROGRAMS "${SAMTOOLS_PROG}" DESTINATION "${THIS_LIBEXECDIR}")
-endif ()
-
 #
 # pyflow
 #