Alternatives to RepeatModeler / nseg install fail

Question

[Jake Warner]

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!

[h.mon]

Did you try to install RepeatModeller using conda?

[Jake Warner]

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."

[h.mon]

Did you try installing with Homebrew?

[Juke34]

I fixed it, so using a repeatmodeler-1.0.11 build pl526_2 and above should be fine now.

[Amaranta_Remedios]

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

Answer 1

[Juke34]

To install nseg (Wooton and Federhen, 1993; see ftp://ftp.ncbi.nih.gov/pub/seg/nseg.
I'm currently trying to fix the bioconda recipe...
There repeatModeler recipe is fixed: repeatmodeler-1.0.11 build pl526_2 and above should be fine.

Answer 2

[Juke34]

I have added nseg in bioconda, you can install it using bioconda now.

Answer 3

[ricardoguerreiro2121]

I would like to help, but make works with me.

This is it's output of doing make in that folder:

cc -g -c genwin.c
genwin.c: In function ‘opendbase’:
genwin.c:95:41: warning: incompatible implicit declaration of built-in function ‘strlen’ [enabled by default]
   dbase->filename = (char *) malloc(strlen(blastdir)+strlen(name)+1);
.......  (does the same for each function in the folder ) .........................

Maybe you need a different version of gcc ? Or some C libraries..

Good luck!