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set(QUASI_INDEX_CMD ${CMAKE_BINARY_DIR}/rapmap quasiindex -t transcripts.fasta -i sample_quasi_index)
execute_process(COMMAND ${QUASI_INDEX_CMD}
WORKING_DIRECTORY ${TOPLEVEL_DIR}/sample_data
RESULT_VARIABLE QUASI_INDEX_RESULT
)
if (QUASI_INDEX_RESULT)
message(FATAL_ERROR "Error running ${QUASI_INDEX_COMMAND}")
endif()
set(MAP_COMMAND ${CMAKE_BINARY_DIR}/rapmap quasimap -t 2 -i sample_quasi_index -1 reads_1.fastq -2 reads_2.fastq -o sample_quasi_map.sam)
execute_process(COMMAND ${MAP_COMMAND}
WORKING_DIRECTORY ${TOPLEVEL_DIR}/sample_data
RESULT_VARIABLE QUASI_MAP_RESULT
)
if (QUASI_MAP_RESULT)
message(FATAL_ERROR "Error running ${QUASI_MAP_RESULT}")
endif()
if (EXISTS ${TOPLEVEL_DIR}/sample_data/sample_quasi_map.sam)
message("RapMap (quasi) ran successfully")
else()
message(FATAL_ERROR "RapMap (quasi-index & map) failed to produce output")
endif()
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