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miso (Python Package)のインストールログ

参照
http://genes.mit.edu/burgelab/miso/docs/#installing-the-fastmiso-version-of-miso(external link)

前提条件(external link)
Required Python modules:
  • Python 2.6 or higher
  • numpy and scipy. Note: MISO requires numpy version > 1.5!
  • pysam, a Python library for working with SAM/BAM files through samtools (Note: MISO requires pysam version 0.6 or higher)
  • matplotlib: Only required for use with sashimi_plot for plotting

Other required software:
  • samtools for accessing SAM/BAM files
  • bedtools: optional, used for computing overlaps and intersections BAM/GFF files by certain features of MISO (like prefiltering and paired-end insert length computation.)


インストール手順:
1.pysamのインストール
$ cd /work_path/
$ wget https://pysam.googlecode.com/files/pysam-0.7.5.tar.gz
$ tar xvfz pysam-0.7.5.tar.gz
$ cd pysam-0.7.5
$ export PYTHONPATH=/installed_python_path/lib/python2.7/site-packages/:$PYTHONPATH
$ /installed_python_path/bin/python setup.py install
...
Finished processing dependencies for pysam==0.7.5


2.MISOのインストール
$ cd /work_path/
$ wget --no-check-certificate http://pypi.python.org/packages/source/m/misopy/misopy-0.4.9.tar.gz
$ tar xvfz misopy-0.4.9.tar.gz
$ cd misopy-0.4.9
$ export PYTHONPATH=/installed_python_path/lib/python2.7/site-packages/:$PYTHONPATH
$ mkdir /tool_path/misopy-0.4.9
$ /installed_python_path/bin/python setup.py install --prefix=/tool_path/misopy-0.4.9


環境の変数PYTHONPATHに、 以下の
MISO_PATH=/tool_path/misopy-0.4.9/lib/python2.6/site-packages
PYTHONPATH=${MISO_PATH}:${PYTHONPATH}


3.インストールのチェック
$ cd /tool_path/misopy-0.4.9 
$ python bin/module_availability.py
Looking for required Python modules..
Checking for availability of: numpy
Checking for availability of: scipy
Checking for availability of: json
Checking for availability of: matplotlib
Checking for availability of: pysam
All modules are available!
Looking for required executables..
Checking if samtools is available
  - samtools is available
Checking if bedtools is available
  - bedtools is available
$ cd /work_path/misopy-0.4.9
$ python misopy/test_miso.py
......
----------------------------------------------------------------------
Ran 3 tests in 70.946s

OK

上のように、「/tool_path/misopy-0.4.9」にインストールしました。
実行ファイルは「/tool_path/misopy-0.4.9/bin」のしたに置く

Last edited by nomonma .
Page last modified on 水曜日 27 of November, 2013 17:34:10 JST.