SplitReadAll_lite.c: Don't hard code the directory location for programs/dirs.
Add the directory location of the needed programs to the $PATH
variable instead of hardcoding them in the script.
Hard coding the paths make it difficult to change the location of those directories.
Or they require that the script is run from a certain working directory.
When adding the directories with those programs to the $PATH variable,
you gain a more easy to change setup.
PATH=/software/samtools:/software/mrsfast:/software/splitread/bin:${PATH}
--- a/SplitReadAll_lite.c
+++ b/SplitReadAll_lite.c
@@ -2,9 +2,10 @@
#include <stdlib.h>
#include <string.h>
-#define mrsFASTexec "./mrsfast/mrsfast" //Location of the executable of the mrsFAST
-#define binarydir "./bin/" //Directory that contains the executables of the SPLITREAD
-#define samtoolsexec "./samtools" //Location of the samtools executable
+// Add the directory location for those programs/dirs to $PATH:
+#define mrsFASTexec "mrsfast" //Location of the executable of the mrsFAST
+#define binarydir "" //Directory that contains the executables of the SPLITREAD
+#define samtoolsexec "samtools" //Location of the samtools executable
int main(int argc, char** argv) {
