Repeatmasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. This installation procedure is based on v4.1.5

Reference:- https://www.repeatmasker.org/RepeatMasker/

Download repeatmasker version 4.1.5 from this link

Copy the downloaded file to the install location and extract in jubail.

$ cp RepeatMasker-4.1.5.tar.gz /scratch/gencore/softwares/
$ cd /scratch/gencore/softwares/
$ tar -xvf RepeatMasker-4.1.5.tar.gz
$ mv RepeatMasker RepeatMasker-4.1.5

Then we would need to install the prerequisites for building this package. We can accomplish this by using the anaconda.

$ module load gencore/1
$ module load Miniconda3/4.7.10
$ conda create -p /scratch/gencore/conda3/envs/repeatmasker4.1.5 -c conda-forge -c bioconda hmmer rmblast trf bioawk -y
$ source activate /scratch/gencore/conda3/envs/repeatmasker4.1.5

Place the RepBase RepeatMasker Edition ( final version 10/26/2018 ) in the install directory and extract the contents.

$ cp /scratch/Reference_Genomes/Public/RepeatMasker/RepBaseRepeatMaskerEdition-20181026.tar.gz /scratch/gencore/softwares/RepeatMasker-4.1.5/
$ cd /scratch/gencore/softwares/RepeatMasker-4.1.5/
$ tar -xvf RepBaseRepeatMaskerEdition-20181026.tar.gz

Download the Dfam 3.7 Library from this link and extract the contents to the Libraries directory.

$ cp /scratch/Reference_Genomes/Public/RepeatMasker/Dfam.h5.gz /scratch/gencore/softwares/RepeatMasker-4.1.5/
$ gunzip Dfam.h5.gz
$ mv Dfam.h5 Libraries/

Run the Configure script as follows:-

$ perl ./configure -libdir /scratch/gencore/software/RepeatMasker-4.1.5/Libraries -trf_prgm /scratch/gencore/conda3/envs/repeatmasker4.1.5/bin/trf
-rmblast_dir /scratch/gencore/conda3/envs/repeatmasker4.1.5/bin/ -hmmer_dir /scratch/gencore/conda3/envs/repeatmasker4.1.5/bin
-abblast_dir /scratch/gencore/conda3/envs/repeatmasker4.1.5/bin -crossmatch_dir /scratch/gencore/conda3/envs/repeatmasker4.1.5/bin
-default_search_engine rmblast

Great, you may see below message once the setup is done.

Building FASTA version of RepeatMasker.lib ......................................................................
Building RMBlast frozen libraries..
The program is installed with a the following repeat libraries:
File: /scratch/gencore/software/RepeatMasker-4.1.5/Libraries/RepeatMaskerLib.h5
FamDB Generator: famdb.py v0.4.2
FamDB Format Version: 0.5
FamDB Creation Date: 2023-01-08 10:42:05.645898

Database: Dfam withRBRM
Version: 3.7
Date: 2023-01-11

To load the modules, follow below procedure.

Launch a new session in jubail.

$ module load gencore/1
$ module load Miniconda3/4.7.10
$ source activate /scratch/gencore/conda3/envs/repeatmasker4.1.5
$ export PATH='/scratch/gencore/software/RepeatMasker-4.1.5:/scratch/gencore/software/RepeatMasker-4.1.5/util':$PATH