I am trying convert my data into gd format for use in the Convert tool under the Genomic Diversity tab. I have a filtered vcf file of all my SNPs already uploaded to Galaxy and was advised to "Custom Build" a reference genome using the reference I used for my original assembly. I have imported the reference .fna (fasta alternative) into Galaxy successfully and it shows up as a reference option when attempting to Convert the SNP file, but the conversion fails each time with this error:
Traceback (most recent call last):
File "/galaxy-repl/instances/main/server/lib/galaxy/jobs/runners/__init__.py", line 590, in finish_job
job_state.job_wrapper.finish( stdout, stderr, exit_code )
File "/galaxy-repl/instances/main/server/lib/galaxy/jobs/__init__.py", line 1232, in finish dataset.set_peek()
File "/galaxy-repl/instances/main/server/lib/galaxy/model/__init__.py", line 1633, in set_peek
return self.datatype.set_peek( self, is_multi_byte=is_multi_byte )
lab/genome_diversity/884ccb07885b/genome_diversity/lib/galaxy/datatypes/wsf.py", line 96, in set_peek
super(Tabular, self).set_peek( dataset, line_count=line_count, is_multi_byte=is_multi_byte, WIDTH='unlimited', skipchars=['#'] )
TypeError: set_peek() got an unexpected keyword argument 'WIDTH'
##I have previously been able to use this tool without indicating a reference sequence but this no longer seems possible.
Any and all help greatly appreciated, thank you,