Skip to content

RepeatModeler (Anaconda)

RepeatModeler is a de-novo transposable element family identification and modelling package.

RepeatModeler is available to install from the Bioconda Anaconda channel.

Installation

Load the default Anaconda module:

module load anaconda3

If required, create a new Conda environment:

mamba create -n myenv

Activate your Conda environment:

mamba activate myenv

In your activated environment, install RepeatModeler from the Bioconda Anaconda channel, additionally specifying the Conda Forge channel for any additional required dependencies:

mamba install -c bioconda -c conda-forge repeatmodeler

Usage

To run the installed version of RepeatModeler, simply load the anaconda3 module and activate your Conda environment:

module load anaconda3
mamba activate myenv

For usage documentation, run RepeatModeler -help:

(myenv) $ RepeatModeler -help
No database indicated

NAME
    RepeatModeler - Model repetitive DNA

SYNOPSIS
      RepeatModeler [-options] -database <XDF Database>

Example jobs

Serial jobs

Here is an example job running on 1 core and 1GB of memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load anaconda3
mamba activate myenv

# create a database for RepeatModeler
BuildDatabase -name DB_NAME INPUT.fa

Here is an example job running on 4 cores and 4GB of memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 4
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load anaconda3
mamba activate myenv

RepeatModeler -database DB_NAME -threads ${NSLOTS}

Core Usage

To ensure that RepeatModeler uses the correct number of cores, the -threads ${NSLOTS} option should be used. Note that the -pa ${REPCORES} method for setting correct threading (as used in previous versions) was deprecated in RepeatModeler 2.0.4.

To request a different number of slots, simply change the core request (smp X value), no additional changes are required.

References