Alternative to DM tools for inbuilt reference sequence

Hi,
Is there any other way other than managing DM Tools for the inbuilt reference genome sequence.
I have found couple questions and answers and related links for the above task. All it says about DM tools.
https://biostar.usegalaxy.org/p/19371/

https://galaxyproject.org/admin/tools/data-managers/

I can’t follow the workshop for DM tools due to lack of prerequisites(knowledge on Unix/Linux command line interface) and also non bioinformatic background. So I would like to know a way to get the sequence of inbuilt reference.
If anybody know or find a way, kindly help with this.

Thank you

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What are your goal(s)?

  1. Install reference genomes into your own Galaxy server?
  2. Learn the source of a particular reference genome available at a public server?
  3. Exact sequence data from a reference genome (based on coordinates) that is already indexed on a server you are working on or some custom reference genome fasta you have in your history?
  4. Other?

Running Data Managers to install genomes is an administrative function, and these can be run with web-based tools or line-command. You would need to be the administrator of the server to install a new built-in genome. The exact genomes installed at usegalaxy.org (and mostly also usegalaxy.eu) are available here: http://datacache.galaxyproject.org/. However, I’m guessing that this is not your goal – am just clarifying how this works/where to find the data.

The Custom Genome/Build functions allow anyone to use a fasta uploaded into a history the same way as a native genome index is used with tools. This is web-based end-user functionality and not an administrative function. FAQ: Preparing and using a Custom Reference Genome or Build

If you just want to extract sequence data from some genome (custom fasta in your history, or indexed genome on the server), then a tool like bedtools GetFastaBed use intervals to extract sequences from a FASTA file is a good choice.

Thanks!

Hi @jennaj,
I have used inbuilt genome in HiSTAT2, followed by String Tie. To use in StringTie merge I require reference annotation to include in the merging (GTF or GFF3 format).

Thank you