how to point to fusion_annotator directory

[anoronh4]

I see that there is an option to use fusionannotator but no way to point to the fusionannotator directory i want to use. looks like i should copy ctat_genome_lib_build_dir to my reference directory but it seems like i can easily point to other reference files so i'm just wondering if i can do that with the CTAT files too.

[mike8115]

Hi @anoronh4,

Currently, the path for the CTAT files are hardcoded in RUN_FusionAnnotator.sh.

MetaFusion/scripts/RUN_FusionAnnotator.sh

Line 12 in 9313317

genome_lib_dir=$(dirname $fusiontools)/reference_files/ctat_genome_lib_build_dir

There's a couple of ways to accomplish what you want. If you plan to stick with a single reference, the easiest solution would be to create a symlink that points to your CTAT files. If you need something more robust and don't mind modifying the code a bit, you could change genome_lib_dir in RUN_FusionAnnotator.sh to accept a positional parameter such as $4 and modify MetaFusion.sh to pass accept a new parameter and pass your specified path to RUN_FusionAnnotator.sh.

MetaFusion/scripts/MetaFusion.sh

Line 176 in 9313317

bash RUN_FusionAnnotator.sh $outdir $cluster $fusiontools

[anoronh4]

thanks so much! if we can use a symlink that's a good workaround for us.