Friday, April 1, 2011

Qiime : Install : HPC

on TALON,
check if python is available
$ what python
/usr/bin/python
Installing Dependencies required for all features of Qiime.
1. Numpy 1.3.0
Source: http://sourceforge.net/projects/numpy/files/NumPy/1.3.0/numpy-1.3.0.tar.gz/download
Dependencies:
1.A. Nose
$ wget http://somethingaboutorange.com/mrl/projects/nose/nose-1.0.0.tar.gz
$ tar zxvf nose-1.0.0.tar.gz 
$ python setup.py install --prefix=$HOME/bin/python
Edit ~/.bashrc and enter the line below
export PYTHONPATH=$PYTHONPATH:$HOME/bin/python
Refresh bash, and check the installation of Nose
$ source ~/.bashrc
$ python -c "import nose"
Untar and install Numpy
$ tar zxvf numpy-1.3.0.tar.gz
$ cd numpy-1.3.0

Download PyCogent-1.5 from http://sourceforge.net/projects/pycogent/files/PyCogent/1.5/PyCogent-1.5.tgz/download
Unpacking and Installing
$ tar zxvf PyCogent-1.5.tgz
$ cd PyCogent-1.5
what

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