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Dear Maker support team</div>
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Thank you so much for developing maker and making it available for researcher like me. </div>
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I am attempting to annotate a genome using your prestigious program. I am running the pipeline on a University server. However, I'm halted by this error "ERROR: Could not determine if RepBase is installed". I have googled it and read on some of the solutions
posted by other researchers such as this one <a href="https://github.com/bioconda/bioconda-recipes/issues/16501" id="LPlnk">
https://github.com/bioconda/bioconda-recipes/issues/16501</a> and many more. </div>
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However, this solution didn't work for me since I'm running Maker on the server and I do not have authority to reinstall nor update programs. I have talked with the University computing team about this error and unfortunately as I suspected the University does
not have a Rebase license which is quite weird for such a big institute. </div>
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<span style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background: var(--white);">But anyways, one of the solutions in this page is to use NCBI WindowMasker instead of RepeatMasker which to requires the RepBase
subscription.</span><br>
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My questions are:</div>
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<ol>
<li>Is possible to use the NCBI WindowMasker within the maker pipeline</li><li>If yes, how do I specify in Maker control files (.exe/opts/bopts) that I would like to use the NCBI WindowMasker instead of
<span style="caret-color:rgb(0, 0, 0);text-align:start;background-color:rgb(255, 255, 255);display:inline !important">
RepeatMasker?</span></li><li>If no to my first question, is there any alternative approach within the Maker pipeline that I can use to annotate repeats beside
<span style="caret-color:rgb(0, 0, 0);text-align:start;background-color:rgb(255, 255, 255);display:inline !important">
RepeatMasker</span>/RepBase?<br>
</li></ol>
<div>Any help would be highly appreciated.</div>
<div>Humble regards </div>
<div>Bongie</div>
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<a target="_blank" id="LPUrlAnchor971639" href="https://github.com/bioconda/bioconda-recipes/issues/16501" style="text-decoration: none; color: var(--themePrimary);">ERROR: Could not determine if RepBase is installed · Issue #16501 · bioconda/bioconda-recipes
· GitHub</a></div>
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Hi @abretaud, @nathanweeks, @johanneskoester, @kastman, @pvanheus, @jerowe, @bgruening and @ArneKr, I ran Maker but I got the following error: > qpeek 4702790.pbs Possible precedence issue with control flow operator at /lustre/work-lustr...</div>
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github.com</div>
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