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RepeatMasker のインストール

~/RepeatMasker/ 以下に RepeatMasker をインストールする方法です。

  1. RepeatMasker をダウンロードします。

    [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
    www.repeatmasker.org をDNSに問いあわせています... 209.124.189.94
    www.repeatmasker.org|209.124.189.94|:80 に接続しています... 接続しました。
    HTTP による接続要求を送信しました、応答を待っています... 200 OK
    長さ: 19122213 (18M) [application/x-gzip]
    `RepeatMasker-open-3-3-0-p1.tar.gz' に保存中

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

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

  2. アーカイブを展開します。

    カレントディレクトリにRepeatMaskerディレクトリが作成されます。 [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. RepeatMasker ライブラリ (Repbase) を入手します (ユーザ登録が必要です。)

    GIRI のサイトから RepeatMasker ライブラリのアーカイブ (repeatmaskerlibraries-20120418.tar.gz) を取得し、~/RepeatMasker/ 以下に設置します。

  4. 取得した RepeatMasker ライブラリのアーカイブを展開します。
    [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 通常ファイル `repeatmaskerlibraries-20120418.tar.gz'? y

  5. 利用している Perl が /usr/local/bin/perl であることを確認します。

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

  6. configure スクリプトを実行し、インストールします。~/RepeatMasker/ 以下に RepeatMasker がインストールされます。

    [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>
    # Enter を押下する

    **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 ]: # Enter を押下する

    **REPEATMASKER INSTALLATION PATH**

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

    Enter path [ /home/username/RepeatMasker ]: # Enter を押下する

      -- 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 ]: # Enter を押下する

    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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