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ccmbioinfo / MetaFusion

GNU Lesser General Public License v3.0
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how to point to fusion_annotator directory #4

Open anoronh4 opened 1 year ago

anoronh4 commented 1 year ago

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 commented 1 year ago

Hi @anoronh4,

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

https://github.com/ccmbioinfo/MetaFusion/blob/9313317ce9463552bd1abde4efe7ce6f3f876d57/scripts/RUN_FusionAnnotator.sh#L12

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.

https://github.com/ccmbioinfo/MetaFusion/blob/9313317ce9463552bd1abde4efe7ce6f3f876d57/scripts/MetaFusion.sh#L176

anoronh4 commented 1 year ago

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