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<p class="MsoNormal">Thanks, Jason!<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">maker-devel <maker-devel-bounces@yandell-lab.org> on behalf of Jason Stajich <jason.stajich@gmail.com><br>
<b>Date: </b>Wednesday, October 6, 2021 at 10:35 AM<br>
<b>To: </b>"Steven L. Miller" <Fungi@uwyo.edu><br>
<b>Cc: </b>"maker-devel@yandell-lab.org" <maker-devel@yandell-lab.org><br>
<b>Subject: </b>Re: [maker-devel] Adapting MAKER pipeline for my HPC<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Steven - <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">You might start with the galaxy install and tutorial or the cyverse one.<o:p></o:p></p>
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<p class="MsoNormal"><a href="https://galaxyproject.github.io/training-material/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html">https://galaxyproject.github.io/training-material/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html</a><o:p></o:p></p>
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<p class="MsoNormal"><a href="https://learning.cyverse.org/projects/sciapps_guide/en/latest/annotation.html">https://learning.cyverse.org/projects/sciapps_guide/en/latest/annotation.html</a><o:p></o:p></p>
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<p class="MsoNormal"><a href="http://gmod.org/wiki/MAKER_Tutorial">http://gmod.org/wiki/MAKER_Tutorial</a><o:p></o:p></p>
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<p class="MsoNormal">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?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">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. <o:p></o:p></p>
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<p class="MsoNormal"><a href="https://funannotate.readthedocs.io/en/latest/">https://funannotate.readthedocs.io/en/latest/</a> - <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">installation with conda <a href="https://funannotate.readthedocs.io/en/latest/install.html">https://funannotate.readthedocs.io/en/latest/install.html</a> <o:p></o:p></p>
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<p class="MsoNormal"> also docker image.<o:p></o:p></p>
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<p class="MsoNormal"><a href="https://hub.docker.com/r/nextgenusfs/funannotate">https://hub.docker.com/r/nextgenusfs/funannotate</a><o:p></o:p></p>
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<p class="MsoNormal"><a href="https://github.com/reslp/funannotate-docker">https://github.com/reslp/funannotate-docker</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Jason Stajich<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Tue, Oct 5, 2021 at 6:17 PM Steven L. Miller <<a href="mailto:Fungi@uwyo.edu">Fungi@uwyo.edu</a>> wrote:<o:p></o:p></p>
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<span style="font-family:"ComicSansMS",serif">Sorry to say probably not a new issue. I saw that MAKER is an easy-to-use genome annotation pipeline </span><span style="color:#222222;background:white">designed to be usable by small research groups with little
bioinformatics experience. That statement describes me to a t. </span><span style="font-family:"ComicSansMS",serif"> 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. </span>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.
<span style="font-family:"ComicSansMS",serif">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). </span><o:p></o:p></p>
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<p class="MsoNormal"> 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.<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"ComicSansMS",serif"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"ComicSansMS",serif">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!<o:p></o:p></span></p>
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<span style="font-family:"ComicSansMS",serif"><o:p> </o:p></span></p>
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<span style="font-family:"ComicSansMS",serif">Sincerely,<br>
Steve Miller<br>
Botany<br>
University of Wyoming<o:p></o:p></span></p>
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<p class="MsoNormal">_______________________________________________<br>
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