[maker-devel] Adapting MAKER pipeline for my HPC

[Mark Yandell]

Thanks, Jason!

From: maker-devel <maker-devel-bounces at yandell-lab.org> on behalf of Jason Stajich <jason.stajich at gmail.com>
Date: Wednesday, October 6, 2021 at 10:35 AM
To: "Steven L. Miller" <Fungi at uwyo.edu>
Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Adapting MAKER pipeline for my HPC

Steven -

You might start with the galaxy install and tutorial or the cyverse one.
https://galaxyproject.github.io/training-material/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html
https://learning.cyverse.org/projects/sciapps_guide/en/latest/annotation.html
http://gmod.org/wiki/MAKER_Tutorial
Not sure if the space needed will be too much for your large genome.  To gain better help you might specify the problems you are having in running or installing?

I'll also point out a parallel genome annotation tool we have built called funannotate which does the prediction training automatically from BUSCO or RNASeq datasets.
https://funannotate.readthedocs.io/en/latest/ -

installation with conda https://funannotate.readthedocs.io/en/latest/install.html
 also docker image.
https://hub.docker.com/r/nextgenusfs/funannotate
https://github.com/reslp/funannotate-docker

Jason Stajich


On Tue, Oct 5, 2021 at 6:17 PM Steven L. Miller <Fungi at uwyo.edu<mailto:Fungi at uwyo.edu>> wrote:

Sorry to say probably not a new issue.  I saw that MAKER is an easy-to-use genome annotation pipeline designed to be usable by small research groups with little bioinformatics experience.  That statement describes me to a t.  I am new to Whole Genome Sequencing and associated analysis, and have a limited skill set with computers.  I have a a 1.52 GB, 75k unitigs, non-photosynthetic vascular plant assembly for which I would like to predict functional genes.  I have tried to follow the tutorial that you have posted for Winter School 2018 to see if I can duplicate your installation and implementation for my HPC.  I doubt that you will be impressed, but I recently received a “certificate” for completing our HPC Linux course path the University of Wyoming. .  I realize now how much I don’t know and how much work it will take to complete an annotation, but I am needing to generate at least some preliminary data to include in an upcoming grant submittal (~2 months).

 I read your MAKER wiki page, but it seems that it hasn’t been completed in many cases, with many important parts (important parts to me, in any case) under construction.

I am writing to get any help I can to find a way forward in my project.  Any suggestions and any help you can provide would be gratefully accepted!



Sincerely,
Steve Miller
Botany
University of Wyoming
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