Harvard:Biophysics 101/2007:Python: Difference between revisions
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*[http://numpy.scipy.org/#older_array Numeric 24.2] ([http://biopython.org/DIST/Numeric-24.2.win32-py2.5.exe direct link to Windows installer]) | *[http://numpy.scipy.org/#older_array Numeric 24.2] ([http://biopython.org/DIST/Numeric-24.2.win32-py2.5.exe direct link to Windows installer]) | ||
'''Installation''' | '''Windows Installation''' | ||
*[http://biopython.org/wiki/Download Download & Install BioPython] | *[http://biopython.org/wiki/Download Download & Install BioPython] | ||
**[http://biopython.org/DIST/biopython-1.42.win32-py2.5.exe direct link to BioPython Windows installer] | **[http://biopython.org/DIST/biopython-1.42.win32-py2.5.exe direct link to BioPython Windows installer] | ||
'''OS X Installation''' | |||
*Install xcode tools (either download ~1GB from the [http://developer.apple.com/tools/download/ developer site]) or install from the OS X installation DVD. | |||
*Download the three dependencies and extract them (double click on the file, or use "tar -xzf filename.tar.gz" for tar.gz files, or "tar -xf filename.tar") | |||
**http://www.egenix.com/files/python/egenix-mx-base-2.0.6.tar.gz | |||
**http://downloads.sourceforge.net/numpy/Numeric-24.2.tar.gz | |||
**http://www.reportlab.org/ftp/ReportLab_2_0.tgz | |||
*For each of the three packages, use a terminal window (/Applications/Utilities/Terminal) to enter the package directory (created when you extracted the files) and run the following commands: | |||
<pre> | |||
python setup.py build | |||
python setup.py install | |||
</pre> | |||
*Download and extract [http://biopython.org/wiki/Download BioPython] source file | |||
**http://biopython.org/DIST/biopython-1.42.tar.gz | |||
*From the extracted directory, run the following commands: | |||
<pre> | |||
python setup.py build | |||
python setup.py test | |||
python setup.py install | |||
</pre> | |||
'''Documentation''' | '''Documentation''' | ||
Revision as of 10:40, 6 February 2007
Python
Installation
Documentation
- Learning Python (for beginners)
- Dive Into Python (for experienced programmers)
- Python Tutorial
- Perl-to-Python
- Python Lib Ref
- Py Reg Ex
BioPython
Pre-installation dependencies
- Python (see above)
- mxTextTools (direct link to Windows installer)
- Numeric 24.2 (direct link to Windows installer)
Windows Installation
OS X Installation
- Install xcode tools (either download ~1GB from the developer site) or install from the OS X installation DVD.
- Download the three dependencies and extract them (double click on the file, or use "tar -xzf filename.tar.gz" for tar.gz files, or "tar -xf filename.tar")
- For each of the three packages, use a terminal window (/Applications/Utilities/Terminal) to enter the package directory (created when you extracted the files) and run the following commands:
python setup.py build python setup.py install
- Download and extract BioPython source file
- From the extracted directory, run the following commands:
python setup.py build python setup.py test python setup.py install
Documentation
