Difference between revisions of "Quick installation instructions for STAMP"
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== Binary release == | == Binary release == | ||
| − | + | An [https://github.com/dparks1134/STAMP/releases/download/v2.1.3/STAMP_2_1_3.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 Linux or OS X using [http://www.virtualbox.org/ Virtual Box]. Due to differences in how the user interface appears under Windows, Linux and OS X we recommended using Virtual Box to run STAMP. 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.python.org/download/ Python 2.5 or 2.6] (we recommend Python 2.6.4) | * [http://www.python.org/download/ Python 2.5 or 2.6] (we recommend Python 2.6.4) | ||
* [http://www.riverbankcomputing.co.uk/software/pyqt/download PyQt4] | * [http://www.riverbankcomputing.co.uk/software/pyqt/download PyQt4] | ||
| − | * [http://www.scipy.org/ NumPy and SciPy] | + | * [http://www.scipy.org/ NumPy and SciPy] |
| − | |||
* [http://matplotlib.sourceforge.net/ matplotlib] | * [http://matplotlib.sourceforge.net/ matplotlib] | ||
| + | * [http://biom-format.org/ biom-format] | ||
| + | * [https://pypi.python.org/pypi/pyqi/ pyqi] | ||
| − | After you have installed Python and the above libraries, extract the [ | + | After you have installed Python and the above libraries, extract the [https://github.com/dparks1134/STAMP/archive/v2.1.3.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 ./bin/STAMP'</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 | + | == Source code on Linux == |
| − | + | STAMP can be install on Linux (tested under Ubuntu 14.04) using the following commands: | |
| + | sudo apt-get install libblas-dev liblapack-dev gfortran | ||
| + | sudo apt-get install freetype* python-pip python-dev python-numpy python-scipy python-matplotlib | ||
| + | sudo pip install STAMP | ||
| − | + | This installs STAMP for use with the default version of Python on your system. You can now run STAMP by entering <tt>'STAMP'</tt> on your command line. | |
| − | + | Note: STAMP requires [http://www.riverbankcomputing.co.uk/software/pyqt/intro PyQt4]. This is install by default on Ubuntu, but may need to be installed independently for different flavours of Linux. | |
| − | + | == Source code on Apple OS X == | |
| − | + | Installation of STAMP on OS X is being driven by community feedback. Please let me know how your experience with installing STAMP of OS X goes so I can update these instructions. | |
| − | + | Our thanks to Tom Battaglia for suggesting the following approach: | |
| − | + | 1. Install Xcode/Command line Tools | |
| − | + | 2. Install the [http://continuum.io/downloads Anaconda] package for Python v2.7 | |
| − | + | 3. Install PIP (if not already on your system): sudo easy_install pip (skip if you already have pip installed) | |
| − | + | 4. Install numpy: pip install numpy | |
| − | + | 5. Install STAMP: pip install STAMP | |
| − | + | 5. Open new terminal session, enter STAMP to run. | |
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== Our build environment == | == Our build environment == | ||
| − | STAMP was developed on Microsoft Windows XP and ported to Apple's | + | STAMP was developed on Microsoft Windows XP and ported to Apple's OS X. [http://www.py2exe.org/ 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. | + | * Python 2.7.3 |
| − | * PyQt4 4.8. | + | * PyQt4 4.8.4 |
| − | * NumPy 1. | + | * NumPy 1.9.1 |
| − | * SciPy 0. | + | * SciPy 0.15.1 |
| − | * | + | * matplotlib 1.4.2 |
| − | * | + | * biom-format 2.0.1 |
| + | * pyqi 0.3.2 | ||
| + | * six 1.8.0 | ||
| + | * h5py 2.3.0 (optional) | ||
* py2exe 0.6.9 | * py2exe 0.6.9 | ||
Latest revision as of 19:31, 25 February 2016
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 Linux or OS X using Virtual Box. Due to differences in how the user interface appears under Windows, Linux and OS X we recommended using Virtual Box to run STAMP. 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:
- Python 2.5 or 2.6 (we recommend Python 2.6.4)
- PyQt4
- NumPy and SciPy
- matplotlib
- biom-format
- pyqi
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 ./bin/STAMP' 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 Linux
STAMP can be install on Linux (tested under Ubuntu 14.04) using the following commands:
sudo apt-get install libblas-dev liblapack-dev gfortran sudo apt-get install freetype* python-pip python-dev python-numpy python-scipy python-matplotlib sudo pip install STAMP
This installs STAMP for use with the default version of Python on your system. You can now run STAMP by entering 'STAMP' on your command line.
Note: STAMP requires PyQt4. This is install by default on Ubuntu, but may need to be installed independently for different flavours of Linux.
Source code on Apple OS X
Installation of STAMP on OS X is being driven by community feedback. Please let me know how your experience with installing STAMP of OS X goes so I can update these instructions.
Our thanks to Tom Battaglia for suggesting the following approach:
1. Install Xcode/Command line Tools 2. Install the Anaconda package for Python v2.7 3. Install PIP (if not already on your system): sudo easy_install pip (skip if you already have pip installed) 4. Install numpy: pip install numpy 5. Install STAMP: pip install STAMP 5. Open new terminal session, enter STAMP to run.
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 2.7.3
- PyQt4 4.8.4
- NumPy 1.9.1
- SciPy 0.15.1
- matplotlib 1.4.2
- biom-format 2.0.1
- pyqi 0.3.2
- six 1.8.0
- h5py 2.3.0 (optional)
- py2exe 0.6.9
