Difference between revisions of "Quick installation instructions for STAMP"

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(Source code on Apple OS X)
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== Binary release ==
 
== Binary release ==
  
An [https://dl.dropboxusercontent.com/u/1339194/STAMP_2_0_1.exe executable binary] is available for  Microsoft Windows. It has been tested under Windows XP SP3 and Windows 7, but will likely also run under Windows Vista. The Windows binary can also be run on OS X using [http://www.virtualbox.org/ Virtual Box]. Due to differences in how the user interface appears under Windows and OS X we recommended using Virtual Box to run STAMP under OS X. Please note that the first time your run STAMP it may take a minute or more to load. After this, it will start up more quickly.  
+
An [https://dl.dropboxusercontent.com/u/1339194/STAMP_2_0_2.exe executable binary] is available for  Microsoft Windows. It has been tested under Windows XP SP3 and Windows 7, but will likely also run under Windows Vista. The Windows binary can also be run on OS X using [http://www.virtualbox.org/ Virtual Box]. Due to differences in how the user interface appears under Windows and OS X we recommended using Virtual Box to run STAMP under OS X. Please note that the first time your run STAMP it may take a minute or more to load. After this, it will start up more quickly.  
  
 
Note: if you have a pristine copy of Microsoft Windows installed, you may need to install the Microsoft Visual C++ 2008 Redistributable Package ([http://www.microsoft.com/downloads/details.aspx?FamilyID=9b2da534-3e03-4391-8a4d-074b9f2bc1bf&displaylang=en 32-bit],[http://www.microsoft.com/downloads/details.aspx?familyid=bd2a6171-e2d6-4230-b809-9a8d7548c1b6&displaylang=en 64-bit]). This package contains a number of commonly required runtime components and as such you likely already have them. STAMP will fail with a message indicating the "configuration is incorrect" if you require this package.
 
Note: if you have a pristine copy of Microsoft Windows installed, you may need to install the Microsoft Visual C++ 2008 Redistributable Package ([http://www.microsoft.com/downloads/details.aspx?FamilyID=9b2da534-3e03-4391-8a4d-074b9f2bc1bf&displaylang=en 32-bit],[http://www.microsoft.com/downloads/details.aspx?familyid=bd2a6171-e2d6-4230-b809-9a8d7548c1b6&displaylang=en 64-bit]). This package contains a number of commonly required runtime components and as such you likely already have them. STAMP will fail with a message indicating the "configuration is incorrect" if you require this package.
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* [http://www.scipy.org/ NumPy and SciPy]  
 
* [http://www.scipy.org/ NumPy and SciPy]  
 
* [http://matplotlib.sourceforge.net/ matplotlib]
 
* [http://matplotlib.sourceforge.net/ matplotlib]
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* [http://biom-format.org/ biom-format
 +
* [https://pypi.python.org/pypi/pyqi/ pyqi]
  
After you have installed Python and the above libraries, extract the [https://dl.dropboxusercontent.com/u/1339194/stamp_2_0_1_src.zip STAMP source code files] to a directory (e.g., C:\STAMP). You can now run STAMP by moving to the source directory and entering <tt>'python STAMP.py'</tt> on your command line. If you get an error message indicating Python cannot be found you likely need to add it to your system path (check out this [http://docs.python.org/using/windows.html#excursus-setting-environment-variables website] for instructions). If you have trouble installing STAMP, please feel free to contact us.
+
After you have installed Python and the above libraries, extract the [https://github.com/dparks1134/STAMP/archive/master.zip STAMP source code files] to a directory (e.g., C:\STAMP). You can now run STAMP by moving to the source directory and entering <tt>'python STAMP.py'</tt> on your command line. If you get an error message indicating Python cannot be found you likely need to add it to your system path (check out this [http://docs.python.org/using/windows.html#excursus-setting-environment-variables website] for instructions). If you have trouble installing STAMP, please feel free to contact us.
  
 
== Source code on Apple OS X ==
 
== Source code on Apple OS X ==
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   import matplotlib
 
   import matplotlib
  
After you have installed Python and the above libraries, extract the [https://dl.dropboxusercontent.com/u/1339194/stamp_2_0_1_src.zip STAMP source code files] to a directory (e.g., ~/STAMP). You can now run STAMP by moving to the source directory and entering <tt>'python STAMP.py'</tt> on your command line.  If you have trouble installing STAMP, please feel free to contact us.
+
After you have installed Python and the above libraries, extract the [https://github.com/dparks1134/STAMP/archive/master.zip STAMP source code files] to a directory (e.g., ~/STAMP). You can now run STAMP by moving to the source directory and entering <tt>'python STAMP.py'</tt> on your command line.  If you have trouble installing STAMP, please feel free to contact us.
  
 
== Source code on Linux ==
 
== Source code on Linux ==
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All other STAMP dependencies will be automatically installed. Please note that many version of Ubuntu (and Linux in general) install matplotlib v0.9.8. STAMP requires version 1.0.1 or greater. You may need to install this separately from [http://matplotlib.sourceforge.net/faq/installing_faq.html#install-from-git source].
 
All other STAMP dependencies will be automatically installed. Please note that many version of Ubuntu (and Linux in general) install matplotlib v0.9.8. STAMP requires version 1.0.1 or greater. You may need to install this separately from [http://matplotlib.sourceforge.net/faq/installing_faq.html#install-from-git source].
  
After you have installed the above libraries, extract the [https://dl.dropboxusercontent.com/u/1339194/stamp_2_0_1_src.zip STAMP source code files] to a directory (e.g., ~/STAMP). You can now run STAMP by moving to the source directory and entering <tt>'python STAMP.py'</tt> on your command line.
+
After you have installed the above libraries, extract the [https://github.com/dparks1134/STAMP/archive/master.zip STAMP source code files] to a directory (e.g., ~/STAMP). You can now run STAMP by moving to the source directory and entering <tt>'python STAMP.py'</tt> on your command line.
  
 
== Command-line interface install ==
 
== Command-line interface install ==
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* matplotlib 1.0.1
 
* matplotlib 1.0.1
 
* py2exe 0.6.9
 
* py2exe 0.6.9
 +
* biom-format 1.3.1
 +
* pyqi 0.3.1

Revision as of 23:35, 5 March 2014

Contents


Binary release

An executable binary is available for Microsoft Windows. It has been tested under Windows XP SP3 and Windows 7, but will likely also run under Windows Vista. The Windows binary can also be run on OS X using Virtual Box. Due to differences in how the user interface appears under Windows and OS X we recommended using Virtual Box to run STAMP under OS X. Please note that the first time your run STAMP it may take a minute or more to load. After this, it will start up more quickly.

Note: if you have a pristine copy of Microsoft Windows installed, you may need to install the Microsoft Visual C++ 2008 Redistributable Package (32-bit,64-bit). This package contains a number of commonly required runtime components and as such you likely already have them. STAMP will fail with a message indicating the "configuration is incorrect" if you require this package.

Source code on Microsoft Windows

STAMP is implemented in Python and running it from source is easy. Any operating system that supports Python should be able to run STAMP from source. Running from source is the best way to fully exploit and contribute to STAMP. STAMP is dependent on the following libraries:

After you have installed Python and the above libraries, extract the STAMP source code files to a directory (e.g., C:\STAMP). You can now run STAMP by moving to the source directory and entering 'python STAMP.py' on your command line. If you get an error message indicating Python cannot be found you likely need to add it to your system path (check out this website for instructions). If you have trouble installing STAMP, please feel free to contact us.

Source code on Apple OS X

Note: OS X user may be experiencing problems running STAMP due to a bug in the latest version of matplotlib. Click here for details. Some user have also found moving from Python 2.6 to Python 2.7 necessary to get all dependencies working.

Installing STAMP from source on Apple OS X is straight-forward. It requires minimal effort on your part, although it does require a lot of compiling. STAMP can be installed from source as follows:

  • Install MacPorts
  • Update MacPorts by typing the following into a console:
 sudo port -d selfupdate 

From your console, install the necessary dependencies for STAMP using port:

 sudo port install python26
 sudo port select --set python python26
 sudo port install py26-sip
 sudo port install py26-macholib
 sudo port install py26-pyqt4
 sudo port install py26-numpy
 sudo port install py26-scipy
 sudo port install py26-matplotlib

Here are some rough estimates on the time required to install each of these packages: python26 = 1 hour, py26-sip = 10 min, py26-macholib = 1 min, py26-pyqt4 = 3 hours, py26-numpy = 3 hours, py26-scipy = 15 min, py26-matplotlib = 5 min.

To test that all dependencies where installed correctly, start a python session and import each package:

 import PyQt4
 import numpy
 import scipy
 import matplotlib

After you have installed Python and the above libraries, extract the STAMP source code files to a directory (e.g., ~/STAMP). You can now run STAMP by moving to the source directory and entering 'python STAMP.py' on your command line. If you have trouble installing STAMP, please feel free to contact us.

Source code on Linux

Heikki Lehvaslaiho has generously suggested the following approach for (K)ubuntu 11.04. From the command line run:

 sudo apt-get install python-scipy python-numpy python-matplotlib pyqt4-dev-tools

All other STAMP dependencies will be automatically installed. Please note that many version of Ubuntu (and Linux in general) install matplotlib v0.9.8. STAMP requires version 1.0.1 or greater. You may need to install this separately from source.

After you have installed the above libraries, extract the STAMP source code files to a directory (e.g., ~/STAMP). You can now run STAMP by moving to the source directory and entering 'python STAMP.py' on your command line.

Command-line interface install

If you wish to use STAMP strictly from the command-line (e.g., as typical of a cluster environment) only the following 3rd-party dependencies are required:

For details on running STAMP from the command-line please see the User's Guide.

Our build environment

STAMP was developed on Microsoft Windows XP and ported to Apple's OS X. py2exe was used to create the Windows binary. It is generally best to download the latest version of each dependency. Our build environment currently uses the following versions of each dependency:

  • Python 2.6.4
  • PyQt4 4.8.4
  • NumPy 1.6.0
  • SciPy 0.9.0
  • matplotlib 1.0.1
  • py2exe 0.6.9
  • biom-format 1.3.1
  • pyqi 0.3.1