Why Isn't RUFUS working?
RUFUS has dependancies on external libraries and resources. If Rufus isn't running properly, it is likely that an external resource cannot be located, or was not built properly.
RUFUS requires both c++11 support as well as the GNU compiler. To ensure RUFUS is compiled correctly, make sure that you are using the gcc compiler, and are using a version thats 4.9.2 or greater to support some gcc compilation flags.
Rufus needs access to the human reference in order to produce a vcf file. If RUFUS is unable to access the human reference, you will see an error message similar to the following:
could not open /uufs/chpc.utah.edu/common/home/u0991464/d1/home/farrelac/RUFUS/bin/gkno_launcher/resources/homo_sapiens/build_37_version_3/human_reference_v37_decoys
To fix this, ensure that there is a human reference file inside the gkno_launcher directory located inside your RUFUS bin.
RUFUS requires the use of samtools, and will not directly build Samtools inside of Rufus. You must be able to run the samtools command from inside your RUFUS directory.
RUFUS may not run correctly due to empty jhash files. If there was an error with the generator files provided, jellyfish will have a run time of 0:00 seconds. If you see any output similar to the following:
then it is likely there was an error in your generator files. Make sure you are providing the correct path to your fasta/fastq files.