Author: Michael R. Crusoe <crusoe@ucdavis.edu>
Description: Use the symbolic name for the build directory, don't hardcode it
Forwarded: https://github.com/COMBINE-lab/salmon/pull/17
--- salmon.orig/cmake/TestSalmon.cmake
+++ salmon/cmake/TestSalmon.cmake
@@ -7,7 +7,7 @@
     message(FATAL_ERROR "Error untarring sample_data.tgz")
 endif()
 
-set(SALMON_INDEX_CMD ${TOPLEVEL_DIR}/build/src/salmon index -t transcripts.fasta -i sample_salmon_index)
+set(SALMON_INDEX_CMD ${CMAKE_BINARY_DIR}/salmon index -t transcripts.fasta -i sample_salmon_index)
 execute_process(COMMAND ${SALMON_INDEX_CMD}
                 WORKING_DIRECTORY ${TOPLEVEL_DIR}/sample_data
                 RESULT_VARIABLE SALMON_INDEX_RESULT
@@ -17,7 +17,7 @@
     message(FATAL_ERROR "Error running ${SALMON_INDEX_COMMAND}")
 endif()
 
-set(SALMON_QUANT_COMMAND ${TOPLEVEL_DIR}/build/src/salmon quant -i sample_salmon_index -l IU -1 reads_1.fastq -2 reads_2.fastq -o sample_salmon_quant -n 1000000)
+set(SALMON_QUANT_COMMAND ${CMAKE_BINARY_DIR}/salmon quant -i sample_salmon_index -l IU -1 reads_1.fastq -2 reads_2.fastq -o sample_salmon_quant -n 1000000)
 execute_process(COMMAND ${SALMON_QUANT_COMMAND}
 	            WORKING_DIRECTORY ${TOPLEVEL_DIR}/sample_data
                 RESULT_VARIABLE SALMON_QUANT_RESULT
