[maker-devel] ERROR: Could not determine if RepBase is installed

[Gumbi,Bonginkosi C]

Dear Maker support team

Thank you so much for developing maker and making it available for researcher like me.

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 https://github.com/bioconda/bioconda-recipes/issues/16501 and many more.
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.

But anyways, one of the solutions in this page is to use NCBI WindowMasker instead of RepeatMasker which to requires the RepBase subscription.
My questions are:

  1.  Is possible to use the NCBI WindowMasker within the maker pipeline
  2.  If yes, how do I specify in Maker control files (.exe/opts/bopts) that I would like to use the NCBI WindowMasker instead of RepeatMasker?
  3.  If no to my first question, is there any alternative approach within the Maker pipeline that I can use to annotate repeats beside RepeatMasker/RepBase?

Any help would be highly appreciated.
Humble regards
Bongie
[https://avatars1.githubusercontent.com/u/14253259?s=400&v=4]<https://github.com/bioconda/bioconda-recipes/issues/16501>

ERROR: Could not determine if RepBase is installed · Issue #16501 · bioconda/bioconda-recipes · GitHub<https://github.com/bioconda/bioconda-recipes/issues/16501>
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...
github.com


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