Question: Alternatives to RepeatModeler / nseg install fail
1
gravatar for Jake Warner
11 months ago by
Jake Warner800
Jake Warner800 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 • 687 views
ADD COMMENTlink modified 10 weeks ago by Juke-343.3k • written 11 months ago by Jake Warner800

Did you try to install RepeatModeller using conda?

ADD REPLYlink written 11 months ago by h.mon29k
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 11 months ago by Jake Warner800

Did you try installing with Homebrew?

ADD REPLYlink written 11 months ago by h.mon29k

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

ADD REPLYlink written 9 weeks ago by Juke-343.3k

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

ADD REPLYlink written 10 months ago by Amaranta_Remedios0
1
gravatar for Juke-34
10 weeks ago by
Juke-343.3k
Sweden
Juke-343.3k 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 9 weeks ago • written 10 weeks ago by Juke-343.3k
1
gravatar for Juke-34
10 weeks ago by
Juke-343.3k
Sweden
Juke-343.3k wrote:

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

ADD COMMENTlink written 10 weeks ago by Juke-343.3k
0
gravatar for ricardoguerreiro2121
5 months ago by
Germany
ricardoguerreiro212140 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 5 months ago by ricardoguerreiro212140
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