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execute_process(COMMAND tar xzvf sample_data.tgz
WORKING_DIRECTORY ${TOPLEVEL_DIR}
RESULT_VARIABLE TAR_RESULT
)
if (TAR_RESULT)
message(FATAL_ERROR "Error untarring sample_data.tgz")
endif()
set(INDEX_CMD ${TOPLEVEL_DIR}/build/src/sailfish index -t transcripts.fasta -k 20 -o sample_index --force)
execute_process(COMMAND ${INDEX_CMD}
WORKING_DIRECTORY ${TOPLEVEL_DIR}/sample_data
RESULT_VARIABLE INDEX_RESULT
)
if (INDEX_RESULT)
message(FATAL_ERROR "Error running ${INDEX_COMMAND}")
endif()
set(QUANT_COMMAND ${TOPLEVEL_DIR}/build/src/sailfish quant -i sample_index --noBiasCorrect -l IU -1 reads_1.fastq -2 reads_2.fastq -o sample_quant)
execute_process(COMMAND ${QUANT_COMMAND}
WORKING_DIRECTORY ${TOPLEVEL_DIR}/sample_data
RESULT_VARIABLE QUANT_RESULT
)
if (QUANT_RESULT)
message(FATAL_ERROR "Error running ${QUANT_RESULT}")
endif()
if (EXISTS ${TOPLEVEL_DIR}/sample_data/sample_quant/quant.sf)
message("Sailfish ran successfully")
else()
message(FATAL_ERROR "Sailfish failed to produce output")
endif()
|
