GTF data in Galaxy

Dear @jennaj I use STAR very often and I noticed that the fasta.gz genome file was used as uncompressed file, but the GTF.gz file wasn’t used as a uncompressed file resulting in a error.
I tried to use the same fasta.gz and gtf uncompressed file directly and run without any problem.
There is any chance set the option gtf/gff file to be used as an uncompressed file automatically?

Have a nice day!

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Hi @Agustin_Baricalla

Data that is in gtf.gz format is automatically uncompressed to gtf during Upload. There is no datatype for gtf.gz – so it wouldn’t be possible to have a dataset with gtf.gz assigned as the datatype. This means there is nothing to implicitly convert compressed to uncompressed at runtime.

If you are not working at a usegalaxy.* server, maybe test out the upload of the data at one of those to better understand the default/supported behavior? Allow Galaxy to autodetect the datatype.

Other Galaxy servers, public or private, may have different custom datatype configurations added, or be running a (much) older Galaxy release, or be running a customized version of this tool. Those admins/tool developers would be the best people to contact if you want a change that fits the custom server environment you are working in.


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