Question: Alternatives to RepeatModeler / nseg install fail
0
gravatar for Jake Warner
6 weeks ago by
Jake Warner690
Jake Warner690 wrote:

Dear All,
I am gearing up for a genome annotation run using MAKER. It is suggested to use a repeat library when running MAKER and as such I am trying to set up RepeatModeler to do so. RepeatModeler relies on program (among several others) called nseg for which I cannot find any documentation. When I try to compile this program with make on OSX I get a slew of warnings and errors. I have no experience in C and can't find any more information so I'm at a loss.

Can anyone recommend alternative software for repeat identification? Please pull me out of this dependency hell!

maker annotation • 146 views
ADD COMMENTlink modified 12 days ago by LLili0 • written 6 weeks ago by Jake Warner690

Did you try to install RepeatModeller using conda?

ADD REPLYlink written 6 weeks ago by h.mon24k

Apparently the conda package doesn't work? From RepeatModeler github:
"WARNING: There is a bioconda and a docker package floating around proporting to have a functional RepeatModeler package. Neither work correctly. For the time being we recommend installing this program as described below."

ADD REPLYlink written 6 weeks ago by Jake Warner690

Did you try installing with Homebrew?

ADD REPLYlink written 6 weeks ago by h.mon24k

I am facing the same problem, did you managed to solve this ?

ADD REPLYlink written 12 days ago by LLili0
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