Hi, I'm using snippy to look for SNPs in my bacterial genomes. Snippy does not seem to be able to recognize my reference genome.gb file (obtained from NCBI). The sample .gbk file from Galaxy's microbial variant calling tutorial is recognized by snippy. Also using a fasta file of my genome works, but I lose gene information. Am I using the wrong file type or am I uploading the files incorrectly to Galaxy?
Quote from the tool form:
--reference [X] Reference genome. Supports FASTA, GenBank, EMBL (not GFF) (default '')
The tool accepts
genbank formatted data. If it is not finding your dataset(s), check to make sure the datatype is set correctly. This is how: https://galaxyproject.org/support/
I am not exactly sure how this tool works but if that is not enough (although it should be) you could try changing the file extension to
.gbk and see if that works. If that is the solution - the tool author can be contacted about the problem through the Tool Shed. This would be considered a bug, but a minor one, with a workaround. Correct datatype assignment should be enough - dataset names should be ignored, with names/extensions used only as labels.
If the tool doesn't work after that, then it depends on where you are using Galaxy. If at some public Galaxy server, contact information is generally on the home landing page. If this your own Galaxy, start by checking the tool install for problems and making sure that Galaxy is current: https://docs.galaxyproject.org/en/master/releases/18.01_announce.html
Thanks! Jen, Galaxy team