Note: This will assume you downloaded the FASTA files to the $SLINKERDIR/references folder.

This should be simple!

1. Navigate to a directory where you want output.

2. Activate that new, fandagnled Slinker environment:
   source activate slinker or conda activate slinker.

3. Insert the following (please adjust for threads and memory to fit your system - the below just seems to do the trick nicely).
   
   bpipe -p case_sample=$SLINKERDIR/tests/unhealthy_Aligned.sortedByCoord.out.bam -p gene=ETV6 -p genome=19 -p a_mem=20000000000 -p g_mem=20000000000 -p results=$PWD -p threads=4 $SLINKERDIR/workflows/slinker.groovy $SLINKERDIR/tests/*.bam

4. Navigate to /your/results/location/plots to see the html and png output.