/ Bio Informatics

installing repeatmasker

there are few pre-requisite things to install repeatmasker..

repeatmasker is the first step involved in the est assembly pipeline

the prerequisites are

----perl
----sequence search engine

you can install one of the three search engines present

-cross-match

-rm blast  ( i am using this one)  http://www.repeatmasker.org/RMBlast.html

-abblast/wublast (these requires licensing )

Try 1. Download pre-compiled versions

$ wget http://www.repeatmasker.org/rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz
$ tar zxvf rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz
$ cd rmblast-1.2-ncbi-blast-2.2.23+
$ cd bin
$ ./rmblastn
./rmblastn: error while loading shared libraries: libpcre.so.0: cannot open shared object file:
No such file or directory

I am unable to install this library. Things i found out, i may be wrong

  • libpcre is part of the 32-bit libraries
  • on ubuntu i was unable to find the library, maybe because of the repository.

Try 2. Download RMBlast source

$ wget http://www.repeatmasker.org/rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz
$ tar zxvf rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz
$ cd rmblast-1.2-ncbi-blast-2.2.23+-src/c++
$ ./configure --with-mt --prefix=/usr/local/rmblast --without-debug
$ make
$ sudo make install

This installed good without any problem Modify ~/.bashrc to include the line below

export PATH=$PATH:/usr/local/rmblast/bin

To check installation

$ source ~/.bashrc
$ rmblastn
BLAST query/options error: Either a BLAST database or subject sequence(s) must be specified

If you get the above message then RMBlast is installed

---- tanden repeat finder (trf) is needed

The TRF download will contain a single executable file. You will need to rename the file from whatever it is to just 'trf' (all lower case). Make TRF executable by typing chmod +x+u trf. You can then move this file wherever you want. I just put it in the /RepeatMasker directory.

the next step is installing repeat database...... it takes 2 days to get registered soo temporarily this process would be out of service.................

after 1 day..........

----Repeatmasker database

$ cd /usr/local
$ wget http://www.repeatmasker.org/RepeatMasker-open-3-2-9.tar.gz
$ tar zxvf RepeatMasker-open-3-2-9.tar.gz

  • It requires RepeatMasker Libraries
    o url: http://www.girinst.org/
    o Go to Downloads > RepeatMasker libraries > RepeatMasker edition: local:

$ tar zxvf repeatmaskerlibraries-20090604.tar.gz
$ rm -rf repeatmaskerlibraries-20090604.tar.gz
$ mv Libraries/RepeatMaskerLib.embl /usr/local/RepeatMasker/Libraries/.

download RepeatMasker
unpack it
install RepeatMasker libraries..copy them into RepeatMasker main folder

now configure the RepeatMasker script by using
perl ./configure

while configuring it would ask for so many where abouts ??
perl path
trf path

after finishing installation
check whether its working or not by typing the command

RepeatMasker in terminal..

Prashanth Madi

Prashanth Madi

I'm a programmer & Tech enthusiast. I work for OpenSource Support Team at Microsoft, but this blog, its content & opinions are my own. I blog about tech, gadgets, code, where we're going & we've been.

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