Description: link against system libraries Author: Dominique Belhachemi Index: tvc-5.0.3+dfsg/CMakeLists.txt =================================================================== --- tvc-5.0.3+dfsg.orig/CMakeLists.txt +++ tvc-5.0.3+dfsg/CMakeLists.txt @@ -2,6 +2,7 @@ cmake_minimum_required (VERSION 2.6) project (ion-tvc) +enable_testing() if("${CMAKE_SYSTEM_PROCESSOR}" STREQUAL "x86_64") set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -msse3") @@ -19,16 +20,12 @@ set(ION_VCFLIB_DIR external/vcflib) set(ION_FREEBAYES_DIR external/freebayes) -set(ION_JSONCPP_DIR external/jsoncpp-src-amalgated0.6.0-rc1) -set(ION_BAMTOOLS_DIR ${PROJECT_BINARY_DIR}/../bamtools-2.4.0.20150702+git15eadb925f) -set(ION_BAMTOOLS_LIBS ${PROJECT_BINARY_DIR}/../bamtools-2.4.0.20150702+git15eadb925f-build/lib/libbamtools.a) -set(ION_ARMADILLO_DIR ${PROJECT_BINARY_DIR}/../armadillo-4.600.1) include_directories(${ION_VCFLIB_DIR}) include_directories(${ION_FREEBAYES_DIR}/src) -include_directories(${ION_JSONCPP_DIR}) -include_directories("${ION_ARMADILLO_DIR}/include") -include_directories("${ION_BAMTOOLS_DIR}/src") + +include_directories("/usr/include/jsoncpp") +include_directories("/usr/include/bamtools") include_directories("${PROJECT_SOURCE_DIR}/VariantCaller") include_directories("${PROJECT_SOURCE_DIR}/VariantCaller/FlowDistEval") @@ -102,7 +99,6 @@ realignment/Realigner.cpp file-io/ion_util.c file-io/ion_error.c - ${ION_JSONCPP_DIR}/jsoncpp.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp ) @@ -112,32 +108,19 @@ endif() add_executable(tvc ${tvcSRCS}) -target_link_libraries(tvc ${ION_BAMTOOLS_LIBS} z pthread blas lapack) +target_link_libraries(tvc bamtools z pthread blas lapack armadillo jsoncpp) add_executable(tvcassembly VariantCaller/IndelAssembly/IndelAssembly.cpp VariantCaller/TargetsManager.cpp VariantCaller/SampleManager.cpp - - # TODO: Actually build vcflib as a static library and link to variant caller. - # TODO2: Resolve bgzf.c collisions between vcflib and bamtools - ${ION_VCFLIB_DIR}/Variant.cpp - ${ION_VCFLIB_DIR}/split.cpp - ${ION_VCFLIB_DIR}/tabixpp/tabix.cpp - ${ION_VCFLIB_DIR}/tabixpp/index.c - ${ION_VCFLIB_DIR}/tabixpp/bgzf.c - ${ION_VCFLIB_DIR}/smithwaterman/LeftAlign.cpp - ${ION_VCFLIB_DIR}/smithwaterman/Repeats.cpp - ${ION_VCFLIB_DIR}/smithwaterman/IndelAllele.cpp - ${ION_VCFLIB_DIR}/smithwaterman/SmithWatermanGotoh.cpp - Util/OptArgs.cpp - ${ION_JSONCPP_DIR}/jsoncpp.cpp + Util/Utils.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp ) -target_link_libraries(tvcassembly ${ION_BAMTOOLS_LIBS} z pthread) +target_link_libraries(tvcassembly bamtools z pthread jsoncpp) add_executable(tvcutils @@ -156,11 +139,10 @@ ${ION_VCFLIB_DIR}/smithwaterman/Repeats.cpp ${ION_VCFLIB_DIR}/smithwaterman/IndelAllele.cpp ${ION_VCFLIB_DIR}/smithwaterman/SmithWatermanGotoh.cpp - ${ION_JSONCPP_DIR}/jsoncpp.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp ) -target_link_libraries(tvcutils ${ION_BAMTOOLS_LIBS} z) +target_link_libraries(tvcutils bamtools z jsoncpp) install(TARGETS tvc DESTINATION bin) install(TARGETS tvcassembly DESTINATION bin) @@ -175,28 +157,111 @@ COMMAND tvc ) -if(0) +if("${CMAKE_SYSTEM_PROCESSOR}" STREQUAL "x86_64") +add_test( tvc_test_1_thread_sse_on + tvc + --input-bam ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/test.bam + --reference ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/reference.fasta + --target-file ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/test_unmerged_detail.bed + --error-motifs ${PROJECT_SOURCE_DIR}/share/TVC/sse/motifset.txt + --use-sse-basecaller on + --trim-ampliseq-primers on + --num-threads 1 + --output-dir ${PROJECT_BINARY_DIR}/test1 + --output-vcf small_variants.vcf +) +endif() + + +add_test( tvc_test_1_thread_sse_off + tvc + --input-bam ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/test.bam + --reference ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/reference.fasta + --target-file ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/test_unmerged_detail.bed + --error-motifs ${PROJECT_SOURCE_DIR}/share/TVC/sse/motifset.txt + --use-sse-basecaller off + --trim-ampliseq-primers on + --num-threads 1 + --output-dir ${PROJECT_BINARY_DIR}/test1 + --output-vcf small_variants.vcf +) + + +if("${CMAKE_SYSTEM_PROCESSOR}" STREQUAL "x86_64") +add_test( tvc_test_4_threads_sse_on_with_parameter_file + tvc + --input-bam ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/test.bam + --reference ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/reference.fasta + --target-file ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/test_unmerged_detail.bed + --error-motifs ${PROJECT_SOURCE_DIR}/share/TVC/sse/motifset.txt + --parameters-file ${PROJECT_SOURCE_DIR}/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json + --use-sse-basecaller on + --trim-ampliseq-primers on + --num-threads 4 + --output-dir ${PROJECT_BINARY_DIR}/test2 + --output-vcf small_variants.vcf +) +endif() + + +add_test( tvc_test_4_threads_sse_off_with_parameter_file + tvc + --input-bam ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/test.bam + --reference ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/reference.fasta + --target-file ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/test_unmerged_detail.bed + --error-motifs ${PROJECT_SOURCE_DIR}/share/TVC/sse/motifset.txt + --parameters-file ${PROJECT_SOURCE_DIR}/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json + --use-sse-basecaller off + --trim-ampliseq-primers on + --num-threads 4 + --output-dir ${PROJECT_BINARY_DIR}/test2 + --output-vcf small_variants.vcf +) add_test(tvcutils_call tvcutils ) +set_tests_properties(tvcutils_call PROPERTIES + PASS_REGULAR_EXPRESSION "Commands" +) add_test(tvcutils_prepare_hotspots_call tvcutils prepare_hotspots ) +set_tests_properties(tvcutils_prepare_hotspots_call PROPERTIES + PASS_REGULAR_EXPRESSION "General options" +) add_test(tvcutils_validate_bed_call tvcutils validate_bed ) +set_tests_properties(tvcutils_validate_bed_call PROPERTIES + PASS_REGULAR_EXPRESSION "General options" +) + +add_test(tvcutils_unify_vcf_call + tvcutils unify_vcf +) +set_tests_properties(tvcutils_unify_vcf_call PROPERTIES + PASS_REGULAR_EXPRESSION "General options" +) + + +add_test(tvcassembly_call + tvcassembly +) + +if(0) -add_test(tvcutils_simple - vcftools - --vcf ./all.merged.vcf - --bed ./effective_regions.bed - --out ./all - --recode - --keep-INFO-all +add_test(pipeline + ${PROJECT_SOURCE_DIR}/bin/variant_caller_pipeline.py + --input-bam ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/test.bam + --reference-fasta ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/reference.fasta + --region-bed ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/test_merged_plain.bed + --primer-trim-bed ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/test_unmerged_detail.bed + --output-dir ${PROJECT_BINARY_DIR}/Testing/variant_caller_pipeline_call ) + add_test(tvc_simple tvc --output-dir ${PROJECT_BINARY_DIR}/Testing/tvc_simple @@ -208,16 +273,9 @@ --num-threads 12 ) -add_test( - variant_caller_pipeline.py - --input-bam ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/test.bam - --reference-fasta ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/reference.fasta - --region-bed ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/test_merged_plain.bed - --primer-trim-bed ${PROJECT_SOURCE_DIR}/share/TVC/examples/example1/test_unmerged_detail.bed - --output-dir ${PROJECT_BINARY_DIR}/Testing/variant_caller_pipeline_call -) endif() +if (0) set(test_rm_files) set(test_file_prefix "AAAA") @@ -251,7 +309,6 @@ ) -if (1) set(test_name variant_caller_pipeline_call) set(test_prog variant_caller_pipeline.py) @@ -280,7 +337,7 @@ endif() -if (1) +if (0) set(test_name Z06-506-CCP) set(test_prog variant_caller_pipeline.py)