Supercomputer

How to Install RepeatMasker

This is the procedure of how to install the RepeatMasker into ~/RepeatMasker/.

1. Download RepeatMasker

   [username@sc090 ~]$ wget http://www.repeatmasker.org/RepeatMasker-open-3-3-0-p1.tar.gz
--2012-11-26 11:40:41-- http://www.repeatmasker.org/RepeatMasker-open-3-3-0-p1.tar.gz
Resolving www.repeatmasker.org... 209.124.189.94
Connecting to www.repeatmasker.org|209.124.189.94|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 19122213 (18M) [application/x-gzip]
Saving to `RepeatMasker-open-3-3-0-p1.tar.gz'

100%[===========================================================>] 19,122,213 321K/s in 79s

2012-11-26 11:42:00 (237 KB/s) - `RepeatMasker-open-3-3-0-p1.tar.gz' saved [19122213/19122213]

2. Unpack Distribution

   The "RepeatMasker" directory will be made in the current working directory. [username@sc090 ~]$ tar xvzf RepeatMasker-open-3-3-0-p1.tar.gz
RepeatMasker/
RepeatMasker/ArrayList.pm
RepeatMasker/RepbaseRecord.pm
...
RepeatMasker/ArrayListIterator.pm
RepeatMasker/ProcessRepeats
RepeatMasker/DeCypherSearchEngine.pm

3. Get the RepeatMasker Library (Repbase)

   To get the library (repeatmaskerlibraries-20120418.tar.gz) you need to register at the GIRI's website. After getting the library, then locate the distribution into the "RepeatMasker" directory.

4. Unpack Distribution

   [username@sc090 ~]$ cd ./RepeatMasker/
[username@sc090 RepeatMasker]$ tar xvzf repeatmaskerlibraries-20120418.tar.gz
Libraries/
Libraries/README.html
Libraries/README
Libraries/RepeatMaskerLib.embl
[username@sc090 RepeatMasker]$ rm repeatmaskerlibraries-20120418.tar.gz
rm: remove regular file `repeatmaskerlibraries-20120418.tar.gz'? y

5. Confirm Perl installation path

   [username@sc090 RepeatMasker]$ which perl
/usr/local/bin/perl

6. Run configure script

   The RepeatMasker will be installed into ~/RepeatMasker/. [username@sc090 RepeatMasker]$ perl ./configure
RepeatMasker Configuration Program

This program assists with the configuration of the
RepeatMasker program. The next set of screens will ask
you to enter information pertaining to your system
configuration. At the end of the program your RepeatMasker
installation will be ready to use.

<PRESS ENTER TO CONTINUE>
# Press Enter

**PERL INSTALLATION PATH**

  This is the full path to the Perl interpreter.
  e.g. /usr/local/bin/perl or enter "env" if you prefer to use
  the "/usr/bin/env perl" mechanism to locate perl.

Enter path [ /usr/local/bin/perl ]: # Press Enter

**REPEATMASKER INSTALLATION PATH**

  This is the path to the location where
  the RepeatMasker program has been installed.

Enter path [ /home/username/RepeatMasker ]: # Press Enter

  -- Building monolithic RM database...

**TRF INSTALLATION PATH**

  This is the path to the location where
  the TRF program can be found. This is used by the RepeatProteinMask program. [NOTE: This script assumes the trf program is called "trf". If it is name trf###-linux.exe you will need to create a symlink called "trf" to it or rename it first.

Enter path [ ]: /usr/local/bin

Add a Search Engine:
   1. CrossMatch: [ Un-configured ]
   2. RMBlast - NCBI Blast with RepeatMasker extensions: [ Un-configured ]
   3. WUBlast/ABBlast (required by DupMasker): [ Un-configured ]
   4. DeCypher (TimeLogic): [ Un-configured ]

   5. Done

Enter Selection: 2

**RMBlast (rmblastn) INSTALLATION PATH**

  This is the path to the location where
  the rmblastn and makeblastdb programs can be found.

Enter path [ ]: /usr/local/package/blast+/2.2.27/bin

Building RMBlast frozen libraries..

Do you want RMBlast to be your default
search engine for Repeatmasker? (Y/N) [ Y ]: # Press Enter

Add a Search Engine:
   1. CrossMatch: [ Un-configured ]
   2. RMBlast - NCBI Blast with RepeatMasker extensions: [ Configured, Default ]
   3. WUBlast/ABBlast (required by DupMasker): [ Un-configured ]
   4. DeCypher (TimeLogic): [ Un-configured ]

   5. Done

Enter Selection: 5

  -- Setting perl interpreter...

Congratulations! RepeatMasker is now ready to use.
The program is installed with a minimal repeat library
by default. This library only contains simple, low-complexity,
and common artefact ( contaminate ) sequences. These are
adequate for use with your own custom repeat library. If you
plan to search using common species specific repeats you will
need to obtain the complete RepeatMasker repeat library from
GIRI ( www.giriinst.org ) and install it in /home/username/RepeatMasker.

Further documentation on the program may be found here:
  /home/username/RepeatMasker/repeatmasker.help


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