Question: Alternatives to RepeatModeler / nseg install fail
1
gravatar for Jake Warner
22 months ago by
Jake Warner810
Jake Warner810 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 • 1.1k views
ADD COMMENTlink modified 13 months ago by Juke344.9k • written 22 months ago by Jake Warner810

Did you try to install RepeatModeller using conda?

ADD REPLYlink written 22 months ago by h.mon32k
2

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 22 months ago by Jake Warner810

Did you try installing with Homebrew?

ADD REPLYlink written 22 months ago by h.mon32k

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

ADD REPLYlink written 13 months ago by Juke344.9k

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

ADD REPLYlink written 21 months ago by Amaranta_Remedios0
1
gravatar for Juke34
13 months ago by
Juke344.9k
Sweden
Juke344.9k wrote:

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.

ADD COMMENTlink modified 13 months ago • written 13 months ago by Juke344.9k
1
gravatar for Juke34
13 months ago by
Juke344.9k
Sweden
Juke344.9k wrote:

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

ADD COMMENTlink written 13 months ago by Juke344.9k
0
gravatar for ricardoguerreiro2121
16 months ago by
Germany
ricardoguerreiro212160 wrote:

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!

ADD COMMENTlink written 16 months ago by ricardoguerreiro212160
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