Import Error with annotating Deseq2 results

1

Hello, I am very new to galaxy and attempting to use Deseq 2 on my first data set. I ran deseq2 with 6 files (3 treated 3 untreated). I got a successful result, however, I then attempted to use the annotating Deseq2 result file tool and I keep getting the error:
“ImportError: cannot import name ‘UnknownSeq’ from ‘Bio.Seq’ (/home/galaxy/database/dependencies/_conda/envs/mulled-v1-61ba501081daf9921383c1402c51e68d5421ca2253eaf7867e6d4de3e09b2263/lib/python3.12/site-packages/Bio/Seq.py”

I am using the hg38 file to compare, and I have used the UCSC and NCBI version, however both ways I continue to get this error. Thank you so much for your time and any insight you can provide on this issue would be much appreciated.

2

Hi @Priya_Das
I am not familiar with this tool, but maybe check if the selected values are present in the annotation file (column 9, attributes).
If you share the history, I can have a look.
Kind regards,
Igor

3

@igor Here is the history. Thank you for your help.

http://cancer-bmv50c3.osumc.edu:8080/u/das31/h/copy-of-copy-of-unnamed-history

4

The GTF file of hg38 that I am using has both exon and mRNA in the 9th column. Would this affect it?

5

Hi @Priya_Das
I cannot connect to the server.
Maybe try the tool on any public Galaxy server, such as usegalaxy.org
It is OK to have accounts on different Galaxy servers.
Kind regards,
Igor

6

I will attempt that. Thank you for your help @igor !

7

There was a long standing and somewhat tricky dependency bug with one of the versions of this tool. It may have shown up at some servers and not others. It was just corrected for any server that pulls in updates from the ToolShed. Thanks for reporting the issue and maybe you and others who had issues before can now run this type of analysis across a wider set of public Galaxy servers! :slight_smile: