Hello, I’m trying to setting up Galaxy on my PC. I need to use the tool “KOBAS annotate” & “KOBAS identify”. I would need help in setting up the field “BLAST protein database” since I don’t understand how to configure it. I tried to download different fasta file from ftp://ftp.ncbi.nlm.nih.gov/blast/db/ but the files inside the “FASTA” directory seems to be not the correct ones and from the main directory I don’t know which one to select. In the server version of Galaxy in this field I used “NCBI NR (22 Jan 2018)” and I would like to use the same on my local installation. Thank you for the help
I also found that installing and using KOBAS locally in Galaxy is not that easy.
Even on https://usegalaxy.org/, the KOBAS database is not fully configured."
Hi @Naibin_Duan
This is the repository for Galaxy. Galaxy | Tool Shed
It uses a much older style of tool wrapper, hasn’t been updated in over five years, the IUC no longer supports it from what I can tell, and the external links to the author website do not resolve. It is probably still on the public servers for legacy reasons.
InterProScan is a better choice given the status.
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I have already downloaded the related databases for KOBAS from here. There are two compressed file packages, sqlite3 and seq_pep (over 52GB in size). I am currently trying to integrate them into the local Galaxy. If successful, I will share the process.
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Great! thanks @Naibin_Duan
@jennaj I once tried downloading and integrating the database to run KOBAS on my local Galaxy platform. However, with the many genome annotation workflows available today, KOBAS is not the optimal choice, so I’ve decided to discontinue using it. I think it’s appropriate to close this thread.
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