右上のdownloadをクリック
cd src/ wget "https://github.com/downloads/taoliu/MACS/MACS-1.4.2-1.tar.gz" --2014-04-06 13:55:08-- https://github.com/downloads/taoliu/MACS/MACS-1.4.2-1.tar.gz github.com をDNSに問いあわせています... 192.30.252.128 github.com|192.30.252.128|:443 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... 302 Found 場所: http://cloud.github.com/downloads/taoliu/MACS/MACS-1.4.2-1.tar.gz [続く] --2014-04-06 13:55:09-- http://cloud.github.com/downloads/taoliu/MACS/MACS-1.4.2-1.tar.gz cloud.github.com をDNSに問いあわせています... 54.230.27.179, 205.251.209.90, 205.251.209.218, ... cloud.github.com|54.230.27.179|: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: 66569 (65K) [application/gzip] `MACS-1.4.2-1.tar.gz' に保存中 100%[======================================>] 66,569 66.4K/s 時間 1.0s 2014-04-06 13:55:11 (66.4 KB/s) - `MACS-1.4.2-1.tar.gz' へ保存完了 [66569/66569]次に解凍 .tar.gzなのでtar jxvfで解凍。-Cで解凍先を指定する。
tar zxvf MACS-1.4.2-1.tar.gz -C ../local/解凍されたMACS-1.4.2-1ディレクトリに移動して、INSTALLファイルをみる
cd ../local/MACS-1.4.2-1 less INSTALL * Prerequisite Python version must be equal to 2.6 or 2.7 to run MACS. We recommend using the version 2.6.5. * Install under Debian or Ubuntu Linux system The most convenient way to install MACS is through Debian APT system, so that it can be perfectly integrated in the Python environment of your operation system. You can easily manage the package, and the uninstall is much easier. Download the deb package from MACS download page, and type this in the commend line: $ dpkg -i macs_1.4.0.deb To uninstall, type: $ dpkg -r macs_1.4.0 MACS uses Python's distutils tools for source installations. To install a source distribution of MACS, unpack the distribution tarball and open up a command terminal. Go to the directory where you unpacked MACS, and simply run the install script : $ python setup.py install By default, the script will install python library and executable codes globally, which means you need to be root or administrator of the machine so as to complete the installation. Please contact the administrator of that machine if you want their help. If you need to provide a nonstandard install prefix, or any other nonstandard options, you can provide many command line options to the install script. Use the –help option to see a brief list of available options: $ python setup.py --help For example, if I want to install everything under my own HOME directory, use this command: $ python setup.py install --prefix /home/taoliu/ようするにpython2.6か2.7が必要。Debian or Ubuntu Linux systemではdpkgというコマンドが使えるようだが、今の環境はCentOSなのでpython setup.py installを使う。prefixを使えば指定先にインストールできる。という事らしい。
python --version Python 2.7.3となったので問題ないかな。
python setup.py install --prefix /home/kosugi/localと叩くと以下のようになり、Python2.7を使っているという事がわかる。
/usr/local/Python-2.7.3/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'console' warnings.warn(msg) /usr/local/Python-2.7.3/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'app' warnings.warn(msg) running install running build running build_py creating build creating build/lib creating build/lib/MACS14 copying lib/__init__.py -> build/lib/MACS14 copying lib/Constants.py -> build/lib/MACS14 copying lib/OptValidator.py -> build/lib/MACS14 copying lib/OutputWriter.py -> build/lib/MACS14 copying lib/PeakDetect.py -> build/lib/MACS14 copying lib/PeakModel.py -> build/lib/MACS14 copying lib/Prob.py -> build/lib/MACS14 creating build/lib/MACS14/IO copying lib/IO/__init__.py -> build/lib/MACS14/IO copying lib/IO/bedGraphIO.py -> build/lib/MACS14/IO copying lib/IO/BinKeeper.py -> build/lib/MACS14/IO copying lib/IO/FeatIO.py -> build/lib/MACS14/IO copying lib/IO/Parser.py -> build/lib/MACS14/IO copying lib/IO/WiggleIO.py -> build/lib/MACS14/IO running build_scripts creating build/scripts-2.7 copying and adjusting bin/macs14 -> build/scripts-2.7 copying and adjusting bin/elandmulti2bed -> build/scripts-2.7 copying and adjusting bin/elandresult2bed -> build/scripts-2.7 copying and adjusting bin/elandexport2bed -> build/scripts-2.7 copying and adjusting bin/sam2bed -> build/scripts-2.7 copying and adjusting bin/wignorm -> build/scripts-2.7 changing mode of build/scripts-2.7/macs14 from 644 to 755 changing mode of build/scripts-2.7/elandmulti2bed from 644 to 755 changing mode of build/scripts-2.7/elandresult2bed from 644 to 755 changing mode of build/scripts-2.7/elandexport2bed from 644 to 755 changing mode of build/scripts-2.7/sam2bed from 644 to 755 changing mode of build/scripts-2.7/wignorm from 644 to 755 running install_lib creating /home/kosugi/local/lib creating /home/kosugi/local/lib/python2.7 creating /home/kosugi/local/lib/python2.7/site-packages creating /home/kosugi/local/lib/python2.7/site-packages/MACS14 copying build/lib/MACS14/__init__.py -> /home/kosugi/local/lib/python2.7/site-packages/MACS14 copying build/lib/MACS14/Constants.py -> /home/kosugi/local/lib/python2.7/site-packages/MACS14 copying build/lib/MACS14/OptValidator.py -> /home/kosugi/local/lib/python2.7/site-packages/MACS14 copying build/lib/MACS14/OutputWriter.py -> /home/kosugi/local/lib/python2.7/site-packages/MACS14 copying build/lib/MACS14/PeakDetect.py -> /home/kosugi/local/lib/python2.7/site-packages/MACS14 copying build/lib/MACS14/PeakModel.py -> /home/kosugi/local/lib/python2.7/site-packages/MACS14 copying build/lib/MACS14/Prob.py -> /home/kosugi/local/lib/python2.7/site-packages/MACS14 creating /home/kosugi/local/lib/python2.7/site-packages/MACS14/IO copying build/lib/MACS14/IO/__init__.py -> /home/kosugi/local/lib/python2.7/site-packages/MACS14/IO copying build/lib/MACS14/IO/bedGraphIO.py -> /home/kosugi/local/lib/python2.7/site-packages/MACS14/IO copying build/lib/MACS14/IO/BinKeeper.py -> /home/kosugi/local/lib/python2.7/site-packages/MACS14/IO copying build/lib/MACS14/IO/FeatIO.py -> /home/kosugi/local/lib/python2.7/site-packages/MACS14/IO copying build/lib/MACS14/IO/Parser.py -> /home/kosugi/local/lib/python2.7/site-packages/MACS14/IO copying build/lib/MACS14/IO/WiggleIO.py -> /home/kosugi/local/lib/python2.7/site-packages/MACS14/IO byte-compiling /home/kosugi/local/lib/python2.7/site-packages/MACS14/__init__.py to __init__.pyc byte-compiling /home/kosugi/local/lib/python2.7/site-packages/MACS14/Constants.py to Constants.pyc byte-compiling /home/kosugi/local/lib/python2.7/site-packages/MACS14/OptValidator.py to OptValidator.pyc byte-compiling /home/kosugi/local/lib/python2.7/site-packages/MACS14/OutputWriter.py to OutputWriter.pyc byte-compiling /home/kosugi/local/lib/python2.7/site-packages/MACS14/PeakDetect.py to PeakDetect.pyc byte-compiling /home/kosugi/local/lib/python2.7/site-packages/MACS14/PeakModel.py to PeakModel.pyc byte-compiling /home/kosugi/local/lib/python2.7/site-packages/MACS14/Prob.py to Prob.pyc byte-compiling /home/kosugi/local/lib/python2.7/site-packages/MACS14/IO/__init__.py to __init__.pyc byte-compiling /home/kosugi/local/lib/python2.7/site-packages/MACS14/IO/bedGraphIO.py to bedGraphIO.pyc byte-compiling /home/kosugi/local/lib/python2.7/site-packages/MACS14/IO/BinKeeper.py to BinKeeper.pyc byte-compiling /home/kosugi/local/lib/python2.7/site-packages/MACS14/IO/FeatIO.py to FeatIO.pyc byte-compiling /home/kosugi/local/lib/python2.7/site-packages/MACS14/IO/Parser.py to Parser.pyc byte-compiling /home/kosugi/local/lib/python2.7/site-packages/MACS14/IO/WiggleIO.py to WiggleIO.pyc running install_scripts copying build/scripts-2.7/macs14 -> /home/kosugi/local/bin copying build/scripts-2.7/elandmulti2bed -> /home/kosugi/local/bin copying build/scripts-2.7/elandresult2bed -> /home/kosugi/local/bin copying build/scripts-2.7/elandexport2bed -> /home/kosugi/local/bin copying build/scripts-2.7/sam2bed -> /home/kosugi/local/bin copying build/scripts-2.7/wignorm -> /home/kosugi/local/bin changing mode of /home/kosugi/local/bin/macs14 to 755 changing mode of /home/kosugi/local/bin/elandmulti2bed to 755 changing mode of /home/kosugi/local/bin/elandresult2bed to 755 changing mode of /home/kosugi/local/bin/elandexport2bed to 755 changing mode of /home/kosugi/local/bin/sam2bed to 755 changing mode of /home/kosugi/local/bin/wignorm to 755 running install_egg_info Writing /home/kosugi/local/lib/python2.7/site-packages/MACS-1.4.2-py2.7.egg-info今回は、/home/kosugi/local/binにemacs14という実行ファイルとその他の実行ファイルが作られている。
elandexport2bed elandmulti2bed elandresult2bed macs14 sam2bed wignormINSTALLファイルにはOn Linux, using bash, I include the new value in my PYTHONPATH by adding this line to my ~/.bashrc となっているので
export PYTHONPATH=/home/kosugi/local/lib/python2.7/site-packages:$PYTHONPATHと記述し再ログインして、macs14とコマンドを叩くと
Usage: macs14 <-t data-blogger-escaped-tfile=""> [-n name] [-g genomesize] [options] Example: macs14 -t ChIP.bam -c Control.bam -f BAM -g h -n test -w --call-subpeaks macs14 -- Model-based Analysis for ChIP-Sequencing Options: 以下オプションの説明となったのでインストール出来た。ヽ(ﾟ∀ﾟ)メ(ﾟ∀ﾟ)メ(ﾟ∀ﾟ)ノ 今回は、インストール先を自分の好きな場所にする事が出来た。--prefix 指定先とすると自動的にbinとlibというディレクトリが作られるようだ。 前もってbinを作ってPATHも通しておいた(ディレクトリの作成)ので、順調に進んだかな。ちゃんとreadmeやinstallといったファイルを見ながら確認してやれば結構敷居低いと感じた。これでChIP-seqの解析できるかな
0 件のコメント:
コメントを投稿