[med-svn] [Git][med-team/marginphase][master] Modify CMakeLists patch
Shayan Doust
gitlab at salsa.debian.org
Tue Jun 23 18:57:57 BST 2020
Shayan Doust pushed to branch master at Debian Med / marginphase
Commits:
f3288ad0 by Shayan Doust at 2020-06-23T18:57:37+01:00
Modify CMakeLists patch
- - - - -
2 changed files:
- + debian/patches/modify_cmakelists.patch
- debian/patches/series
Changes:
=====================================
debian/patches/modify_cmakelists.patch
=====================================
@@ -0,0 +1,262 @@
+Description: modify CMakeLists
+ We need to link statically to libson, and specify various include directories as we are building and linking against debian-packaged libraries.
+Author: Shayan Doust <hello at shayandoust.me>
+Last-Update: 2020-06-23
+---
+
+--- marginphase.orig/CMakeLists.txt
++++ marginphase/CMakeLists.txt
+@@ -12,181 +12,11 @@
+ # set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")
+ #endif()
+
+-set(HTSLIB_HEADERS
+- externalTools/htslib
+- externalTools/htslib/htslib
+- externalTools/htslib/cram
+- externalTools/htslib/os
+- )
+-set(SONLIB_HEADERS
+- externalTools/sonLib/C/inc
+- externalTools/sonLib/C/impl
+- externalTools/sonLib/C/tests
+- externalTools/sonLib/externalTools/cutest
+- externalTools/sonLib/externalTools/quicktree_1.1/include
+- )
+-
+-include_directories(inc)
+-include_directories(${HTSLIB_HEADERS})
+-include_directories(${SONLIB_HEADERS})
+-include_directories(externalTools/jsmn)
+-
+-set(HTSLIB_SOURCES
+- externalTools/htslib/cram/cram_codecs.c
+- externalTools/htslib/cram/cram_decode.c
+- externalTools/htslib/cram/cram_encode.c
+- externalTools/htslib/cram/cram_external.c
+- externalTools/htslib/cram/cram_index.c
+- externalTools/htslib/cram/cram_io.c
+- externalTools/htslib/cram/cram_samtools.c
+- externalTools/htslib/cram/cram_stats.c
+- externalTools/htslib/cram/files.c
+- externalTools/htslib/cram/mFILE.c
+- externalTools/htslib/cram/open_trace_file.c
+- externalTools/htslib/cram/pooled_alloc.c
+- externalTools/htslib/cram/rANS_static.c
+- externalTools/htslib/cram/sam_header.c
+- externalTools/htslib/cram/string_alloc.c
+- externalTools/htslib/os/rand.c
+- externalTools/htslib/test/fieldarith.c
+- externalTools/htslib/test/hfile.c
+- externalTools/htslib/test/hts_endian.c
+- externalTools/htslib/test/sam.c
+- externalTools/htslib/test/test-bcf-sr.c
+- externalTools/htslib/test/test-regidx.c
+- externalTools/htslib/test/test-vcf-api.c
+- externalTools/htslib/test/test-vcf-sweep.c
+- externalTools/htslib/test/test_bgzf.c
+- externalTools/htslib/test/test_view.c
+- externalTools/htslib/test/thrash_threads1.c
+- externalTools/htslib/test/thrash_threads2.c
+- externalTools/htslib/test/thrash_threads3.c
+- externalTools/htslib/test/thrash_threads4.c
+- externalTools/htslib/test/thrash_threads5.c
+- externalTools/htslib/test/thrash_threads6.c
+- externalTools/htslib/bcf_sr_sort.c
+- externalTools/htslib/bgzf.c
+- externalTools/htslib/bgzip.c
+- externalTools/htslib/errmod.c
+- externalTools/htslib/faidx.c
+- externalTools/htslib/hfile.c
+- externalTools/htslib/hfile_gcs.c
+- externalTools/htslib/hfile_libcurl.c
+- externalTools/htslib/hfile_net.c
+- externalTools/htslib/hfile_s3.c
+- externalTools/htslib/hts.c
+- externalTools/htslib/htsfile.c
+- externalTools/htslib/kfunc.c
+- externalTools/htslib/knetfile.c
+- externalTools/htslib/kstring.c
+- externalTools/htslib/md5.c
+- externalTools/htslib/multipart.c
+- #externalTools/htslib/plugin.c
+- externalTools/htslib/probaln.c
+- externalTools/htslib/realn.c
+- externalTools/htslib/regidx.c
+- externalTools/htslib/sam.c
+- externalTools/htslib/synced_bcf_reader.c
+- externalTools/htslib/tabix.c
+- externalTools/htslib/tbx.c
+- externalTools/htslib/textutils.c
+- externalTools/htslib/thread_pool.c
+- externalTools/htslib/vcf.c
+- externalTools/htslib/vcf_sweep.c
+- externalTools/htslib/vcfutils.c
+- )
+-
+-set(SONLIB_SOURCES
+- externalTools/sonLib/C/impl/avl.c
+- externalTools/sonLib/C/impl/bioioC.c
+- externalTools/sonLib/C/impl/commonC.c
+- externalTools/sonLib/C/impl/fastCMaths.c
+- externalTools/sonLib/C/impl/hashTableC.c
+- externalTools/sonLib/C/impl/hashTableC_itr.c
+- externalTools/sonLib/C/impl/lz4.c
+- externalTools/sonLib/C/impl/lz4hc.c
+- externalTools/sonLib/C/impl/pairwiseAlignment.c
+- externalTools/sonLib/C/impl/sonLibAlign.c
+- externalTools/sonLib/C/impl/sonLibCache.c
+- externalTools/sonLib/C/impl/sonLibCommon.c
+- externalTools/sonLib/C/impl/sonLibCompression.c
+- externalTools/sonLib/C/impl/sonLibConnectivity.c
+- externalTools/sonLib/C/impl/sonLibEulerTour.c
+- externalTools/sonLib/C/impl/sonLibExcept.c
+- externalTools/sonLib/C/impl/sonLibFile.c
+- externalTools/sonLib/C/impl/sonLibHash.c
+- externalTools/sonLib/C/impl/sonLibKVDatabase.c
+- externalTools/sonLib/C/impl/sonLibKVDatabase_BigRecordFile.c
+- externalTools/sonLib/C/impl/sonLibKVDatabase_KyotoTycoon.cpp
+- externalTools/sonLib/C/impl/sonLibKVDatabase_MySql.c
+- externalTools/sonLib/C/impl/sonLibKVDatabase_TokyoCabinet.c
+- externalTools/sonLib/C/impl/sonLibKVDatabaseConf.c
+- externalTools/sonLib/C/impl/sonLibList.c
+- externalTools/sonLib/C/impl/sonLibMath.c
+- externalTools/sonLib/C/impl/sonLibNaiveConnectivity.c
+- externalTools/sonLib/C/impl/sonLibRandom.c
+- externalTools/sonLib/C/impl/sonLibSet.c
+- externalTools/sonLib/C/impl/sonLibSortedSet.c
+- externalTools/sonLib/C/impl/sonLibString.c
+- externalTools/sonLib/C/impl/sonLibTreap.c
+- externalTools/sonLib/C/impl/sonLibTree.c
+- externalTools/sonLib/C/impl/sonLibTuples.c
+- externalTools/sonLib/C/impl/stGraph.c
+- externalTools/sonLib/C/impl/stMatrix.c
+- externalTools/sonLib/C/impl/stPhylogeny.c
+- externalTools/sonLib/C/impl/stPosetAlignment.c
+- externalTools/sonLib/C/impl/stSafeC.c
+- externalTools/sonLib/C/impl/stThreadPool.c
+- externalTools/sonLib/C/impl/stUnionFind.c
+- externalTools/sonLib/C/tests/allTests.c
+- externalTools/sonLib/C/tests/cigarsTest.c
+- externalTools/sonLib/C/tests/fastaCTest.c
+- #externalTools/sonLib/C/tests/kt_connect_test.cpp
+- externalTools/sonLib/C/tests/kvDatabaseTest.c
+- externalTools/sonLib/C/tests/kvDatabaseTestCommon.c
+- externalTools/sonLib/C/tests/sonLibAlignTest.c
+- externalTools/sonLib/C/tests/sonLibCacheTest.c
+- externalTools/sonLib/C/tests/sonLibCommonTest.c
+- externalTools/sonLib/C/tests/sonLibCompressionTest.c
+- externalTools/sonLib/C/tests/sonLibConnectivityTests.c
+- externalTools/sonLib/C/tests/sonLibDoubleTuplesTest.c
+- externalTools/sonLib/C/tests/sonLibEdgeContainerTests.c
+- externalTools/sonLib/C/tests/sonLibEulerTest.c
+- externalTools/sonLib/C/tests/sonLibExceptTest.c
+- externalTools/sonLib/C/tests/sonLibFileTest.c
+- externalTools/sonLib/C/tests/sonLibGraphTest.c
+- externalTools/sonLib/C/tests/sonLibHashTest.c
+- externalTools/sonLib/C/tests/sonLibIntTuplesTest.c
+- externalTools/sonLib/C/tests/sonLibListTest.c
+- externalTools/sonLib/C/tests/sonLibPosetAlignmentTest.c
+- externalTools/sonLib/C/tests/sonLibRandomTest.c
+- externalTools/sonLib/C/tests/sonLibSetTest.c
+- externalTools/sonLib/C/tests/sonLibSortedSetTest.c
+- externalTools/sonLib/C/tests/sonLibStringTest.c
+- externalTools/sonLib/C/tests/sonLibTreapTest.c
+- externalTools/sonLib/C/tests/sonLibTreeTest.c
+- externalTools/sonLib/C/tests/sonLibTuplesTest.c
+- externalTools/sonLib/C/tests/stMatrixTest.c
+- externalTools/sonLib/C/tests/stPhylogenyTest.c
+- externalTools/sonLib/C/tests/stThreadPoolTest.c
+- externalTools/sonLib/C/tests/stUnionFindTest.c
+- externalTools/sonLib/externalTools/cutest/AllTests.c
+- externalTools/sonLib/externalTools/cutest/CuTest.c
+- externalTools/sonLib/externalTools/cutest/CuTestTest.c
+- externalTools/sonLib/externalTools/quicktree_1.1/src/align.c
+- externalTools/sonLib/externalTools/quicktree_1.1/src/aln2dist.c
+- externalTools/sonLib/externalTools/quicktree_1.1/src/aln2tree.c
+- externalTools/sonLib/externalTools/quicktree_1.1/src/buildtree.c
+- externalTools/sonLib/externalTools/quicktree_1.1/src/cluster.c
+- externalTools/sonLib/externalTools/quicktree_1.1/src/dist2tree.c
+- externalTools/sonLib/externalTools/quicktree_1.1/src/distancemat.c
+- externalTools/sonLib/externalTools/quicktree_1.1/src/distancemat_merops.c
+- externalTools/sonLib/externalTools/quicktree_1.1/src/options.c
+- externalTools/sonLib/externalTools/quicktree_1.1/src/quicktree.c
+- externalTools/sonLib/externalTools/quicktree_1.1/src/sequence.c
+- externalTools/sonLib/externalTools/quicktree_1.1/src/tree.c
+- externalTools/sonLib/externalTools/quicktree_1.1/src/util.c
+- )
++include_directories(inc/)
++include_directories(/usr/include/htslib/)
++include_directories(/usr/include/sonlib/)
++include_directories(/usr/include/quicktree/)
++include_directories(/usr/include/)
+
+ set(SOURCE_FILES
+ impl/column.c
+@@ -203,63 +33,14 @@
+ impl/vcfTools.c
+ )
+
+-
+-# Dependencies for htslib
+-find_library(ZLIB NAMES z)
+-if(${ZLIB} STREQUAL "ZLIB-NOTFOUND")
+- message(FATAL_ERROR "Couldn't find the 'z' library")
+-endif()
+-
+-find_library(BZ2LIB bz2)
+-if(${BZ2LIB} STREQUAL "BZ2LIB-NOTFOUND")
+- message(FATAL_ERROR "Couldn't find the 'bz2' library")
+-endif()
+-
+-find_library(LZMALIB lzma)
+-if(${LZMALIB} STREQUAL "LZMALIB-NOTFOUND")
+- message(FATAL_ERROR "Couldn't find the 'lzma' library")
+-endif()
+-
+-find_library(CURLLIB curl)
+-if(${CURLLIB} STREQUAL "CURLLIB-NOTFOUND")
+- message(FATAL_ERROR "Couldn't find the 'curl' library")
+-endif()
+-
+-find_library(CRYPTOLIB crypto)
+-if(${CRYPTOLIB} STREQUAL "CRYPTOLIB-NOTFOUND")
+- message(FATAL_ERROR "Couldn't find the 'crypto' library")
+-endif()
+-
+-find_library(PTHREADLIB pthread)
+-if(${PTHREADLIB} STREQUAL "PTHREADLIB-NOTFOUND")
+- message(FATAL_ERROR "Couldn't find the 'pthread' library")
+-endif()
+-
+-add_custom_command(
+- OUTPUT "${PROJECT_SOURCE_DIR}/externalTools/htslib/config.h"
+- COMMAND autoconf
+- COMMAND autoheader
+- COMMAND ./configure
+- COMMAND make
+- WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/externalTools/htslib/
+-)
+-add_custom_target(HTSLIB_CONFIGURED DEPENDS "${PROJECT_SOURCE_DIR}/externalTools/htslib/config.h")
+-
+-add_library(son ${SONLIB_SOURCES})
+-add_library(hts ${HTSLIB_SOURCES})
+-add_dependencies(hts HTSLIB_CONFIGURED)
+-add_library(jsmn externalTools/jsmn/jsmn.c)
+-
+-target_link_libraries(hts pthread crypto bz2 lzma z curl)
+-
+ add_executable(marginPhase marginPhase.c ${SOURCE_FILES})
+-target_link_libraries(marginPhase son hts jsmn)
++target_link_libraries(marginPhase -lm /usr/lib/x86_64-linux-gnu/sonLib.a hts)
+
+ add_executable(vcfCompare vcfCompare.c ${SOURCE_FILES})
+-target_link_libraries(vcfCompare son hts jsmn)
++target_link_libraries(vcfCompare -lm /usr/lib/x86_64-linux-gnu/sonLib.a hts)
+
+
+ enable_testing()
+ add_executable(allTests tests/allTests.c tests/marginPhaseTest.c tests/stRPHmmTest.c tests/parserTest.c ${SOURCE_FILES})
+-target_link_libraries(allTests hts son jsmn)
++target_link_libraries(allTests -lm hts /usr/lib/x86_64-linux-gnu/sonLib.a)
+ add_test(stRPHmm allTests)
=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
+modify_cmakelists.patch
include_private_header.patch
View it on GitLab: https://salsa.debian.org/med-team/marginphase/-/commit/f3288ad006951b23bd39a4828d28b7974a8564f2
--
View it on GitLab: https://salsa.debian.org/med-team/marginphase/-/commit/f3288ad006951b23bd39a4828d28b7974a8564f2
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