This page was last updated on Sunday, 20-Nov-2016 11:43:46 CST

Installation notes for RepeatMasker version 4-0-5

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Prerequisites

• RMBlast
  1. $ ver="2.2.28"
  2. $ cd /programinstallers/
  3. $ wget -N ftp://ftp.ncbi.nlm.nih.gov/blast/executables/rmblast/LATEST/ncbi-rmblastn-$ver-x64-linux.tar.gz
  4. $ tar -zxvf ncbi-rmblastn-$ver-x64-linux.tar.gz
  5. $ sudo cp -puv ncbi-rmblastn-$ver/bin/rmblastn /usr/bin/
  6. We don't need any other files from this
     $ rm ncbi-rmblastn-$ver -rf
• Blast+
• TRF
  1. $ ver="407b"
  2. $ cd /programinstallers/
  3. I had to download from the web page, since the link is obscured
  4. Program must be named trf exactly for RepeatMasker to find it
     $ cp -puv trf$ver.linux64 /usr/local/bin/trf
  5. $ chmod +x /usr/local/bin/trf

Installation

1. $ ver="4-0-5"
2. $ cd /programinstallers/
3. $ wget -N http://www.repeatmasker.org/RepeatMasker-open-$ver.tar.gz
4. $ cd /usr/local/bin
5. If upgrading, first remove or rename /usr/local/bin/RepeatMasker
6. $ tar -zxvf /programinstallers/RepeatMasker-open-$ver.tar.gz
7. Install the standard repeat library
   Through web browser, go to http://www.girinst.org/server/RepBase/index.php, log in, and download remasker database, for example repeatmaskerlibraries-20140131.tar.gz
8. $ cd /usr/local/bin/RepeatMasker
9. $ tar -zxvf /programinstallers/repeatmaskerlibraries-20140131.tar.gz
   

   Libraries/
   Libraries/RepeatMaskerLib.embl
   Libraries/RepeatAnnotationData.pm
   Libraries/README.html
   Libraries/taxonomy.dat
   Libraries/README

10. Add our custom libraries to /usr/local/bin/RepeatMasker/Libraries/
11. Configure
    $ perl ./configure
    NOTE: when the configure programs asks for the path for RMBlast, do not include the full path with the program name, e.g. /usr/bin/rmblastn, use just the path /usr/bin, or else you will get the confusing error message
    /usr/bin/rmblastn does not exist
    even though it does exist.
    

     -- Setting perl interpreter...
    
    Congratulations!  RepeatMasker is now ready to use.
    The program is installed with a full version of the repeat library:
      DFAM Library Version = Dfam_1.2
      RMLibrary Version = 20140131
      Repbase Version = 20140131
    Further documentation on the program may be found here:
      /usr/local/bin/RepeatMasker/repeatmasker.help
    

12. Add to default PATH
    $ sudo nano /etc/profile
    …
    PATH="$PATH:/usr/local/bin/RepeatMasker"
    …