Perform these steps to download and install Python, IDLE, Tkinter, NumPy, and PyGame: Browse to the Python for Mac download page. In the resulting page click on the Download Python 3.6.5 button. Your browser will download the file python-3.6.5-macosx10.6.pkg to your Downloads directory. Download the macOS Sierra installer Launch the App Store app, then look for macOS Sierra in the store. (Here’s a link.) Click on the Download button, and your Mac will download the installer to. The easiest way is to download the Python installer from the python.org website. Visit Python.org and download the latest available Python installer file; Run the downloaded file and install Python 3.x on Mac. Python 3.6.x requires about 100MB of available disk space. Chris Breen’s 2012 directions on using SSH to reboot or shutdown a Mac via a Terminal session remain accurate, so I refer you there. But creating a remote Terminal session via SSH, a secure.
Optional AltAnalyze Dependencies to be Installed
The compiled versions of AltAnalyze (Windows, Mac OSX and Ubuntu) should run immediately after extraction, however, the source code implementations may require additional Python modules installed. These are:
- Required: Python version 2.3 or greater
- Graphical User Interface requirement: Tkinter
- WikiPathways API visualization: lxml
- Faster Fisher Exact Test: Scipy
- Visualization output files: Matplotlib, Numpy, Scipy
- PNG viewing in the GUI: Python Imaging Library (PIL) ImageTk
- Statistical libraries for Combat: Patsy and Pandas
- Network visualization in igraph: igraph and cairo
These libraries can be installed from source code or from installers provided by the open-source project websites.
To determine if a pre-compiled version of AltAnalyze is compatible with your operating system, download the program and double-click the executable file name 'AltAnalyze'. The program can also be initiated from a terminal command-line (e.g., './AltAnalyze in Linux). Feel free to contact us about any problems.
Instructions for Windows/Linux/Mac OS X
![Tkinter Tkinter](/uploads/1/2/6/7/126707478/107871481.png)
Mac OS X
By default, Mac OS X has Python installed along with Tkiner. Python version 2X should be default and used instead of python 3.
Windows
Install Python 2.7 from http://www.python.org. Tkinter is installed by default.
Linux (see Ubuntu below)
If python or tkinter is not installed, install Python 2.7 from http://www.python.org. Tkinter is installed by default. Test by typing
python
at the terminal and then import tkinter
.Cross-Platform Installation Options
Python and Tkinter are all that are needed for AltAnalyze to run, but other dependencies are required if you wish to visualize WikiPathways (suds, PIL), cluster or QC plots (Matplotlib, Numpy, Scipy) or speed up the Fisher Exact Test analysis (scipy). To install these, see the below instructions.
- Install setuptools: http://pypi.python.org/pypi/setuptools/
- Install suds:
sudo easy_install suds
- Install matplotlib:
sudo easy_install matplotlib
- Install numpy:
sudo easy_install numpy
- Install scipy:
sudo easy_install scipy
- Install Imagetk:
easy_install --find-links http://www.pythonware.com/products/pil/ Imaging
- Install patsy:
sudo easy_install patsy
- Install pandas:
sudo easy_install pandas
- Install fastcluster: recommend install from source
- Install igraph: recommend installer
- Install cairo: recommend install from source (see INSTALL file or here for Windows users)
- Install ordereddict (Python 2.6 or below) :
easy_install ordereddict
Instructions for Ubuntu
Adding support for python applications call Tk is particularly challenging on Ubuntu, since Python is installed but Tkinter is not. We recommend:
- Ensure all Ubuntu updates have been installed
- Install Tkinter:
apt-get install python-tk
(restart after) - Install setuptools:
sudo apt-get install python-setuptools
- Install suds:
sudo easy_install suds
- Install matplotlib:
sudo apt-get install python-matplotlib
- Install numpy:
sudo apt-get install python-numpy
- Install scipy:
sudo apt-get install python-scipy
- Install Imagetk:
sudo apt-get install python-imaging python-imaging-tk
- Install patsy:
sudo easy_install patsy
- Install pandas:
sudo easy_install pandas
- Install fastcluster:
sudo easy_install fastcluster
Note: Installing from source is necessary when
apt-get
or easy_install
does not properly obtain all dependent libraries. To install from source use these commands:python setup.py build
sudo python setup.py install
For igraph, install as described here
- This will install to the default system python (default or python installed by
apt-get
). If installed via other means (e.g., from source to /usr/local/bin), you will need to sym link the igraph folder from the equivalent system python version to your local installed and use the commandexport LD_LIBRARY_PATH=/usr/lib/
orexport LD_LIBRARY_PATH=/usr/local/lib/
if igraph gives an ImportError.
Developers Only
Both PyInstaller and cx_Freeze have been used to build AltAnalyze binary distributions. In general, PyInstaller works the best with the described patch for Ubuntu, whereas cx_Freeze will work for some but not all Ubuntu releases and configurations (e.g., compatible with 10.04).
- Install cx_Freeze from source (problems with
apt-get
) (may require libssl-dev be installed) - OR download and extract PyInstaller 1.6 (requires this patch)
- In the AltAnalyze main program directory (ensure .py files are in this root and not just Source_code), run:
python setup.py build
- Paste the files in the build/exe.linux directory into the AltAnalyze main program folder.
- Test the 'AltAnalyze' executable file in a copy of the AltAnalyze directory prior to distribution.
Creating Compilers (advanced)
If you wish to create your own compiled version of AltAnalyze for distribution to your users (e.g., custom versions or unsupported operating systems), install the above and be mindful of the following:
- Customization of the
setup.py
file may be required for inclusion or exclusion of OS specific libraries (dll files). - See the
setup.py
script for run instructions on different operating systems. - The suds package folder must exist in the Python site-packages folder (not just the egg - zip must be extracted).
- Issues with matplotlib external dependencies may occur (see existing
setup.py
files for details). - Issues with conflicting dependencies may occur on some OSs resulting in strange errors during binary creations. These include: the python library six may need to be called as site-packages/six/six.py rather than the egg file.
Potential Issues
- Pandas installs it's own dateutil which may cause errors to be displayed in the console and possibly other issues.
Important
If you are using a Python from any current python.orgPython installer for macOS (3.8.0+, 3.7.2+, 3.6.8, or 2.7.16+),no further action is needed to use IDLE or tkinter.A built-in version of Tcl/Tk 8.6 will be used.
If you are using macOS 10.6 or later, the Apple-suppliedTcl/Tk 8.5 has serious bugs that can cause application crashes.If you wish to use IDLE or Tkinter, do not use the Apple-suppliedPythons. Instead, install and use a newer version of Pythonfrom python.org or a third-party distributor that supplies orlinks with a newer version of Tcl/Tk.
Python's integrated development environment,IDLE, and thetkinter GUI toolkitit uses, depend on the Tk GUI toolkit which isnot part of Python itself. For best results, it is important that theproper release of Tcl/Tk is installed on your machine.For recent Python installers for macOS downloadable from this website,here is a summary of current recommendations followed by more detailedinformation.
PythonRelease | InstallerVariant | macOSRelease | RecommendedTcl/Tk | AlternateTcl/Tk | NotRecommended |
---|---|---|---|---|---|
3.8.5,3.7.9,2.7.18 | all | 10.9 to10.15 | built-in8.6.8 |
There are currently three major variants of Tk in common use on macOS:
- Aqua Cocoa Tk
- A newer native implementation availableas a universal 64-bit and 32-bit binary. This variant is the standard nativemacOS variant in Tk 8.6 and as of Tk 8.5.13. Aqua Cocoa support wasbackported to Tk 8.5 (prior to 8.5.13) and released by Apple starting with macOS 10.6and by ActiveState starting with their 8.5.9.1 release.
- Aqua Carbon Tk
- Because it is implemented with older macOS Carbon interfaces, it isonly available as a 32-bit binary (usually for Intel and PowerPCprocessors). Aqua Carbon Tk 8.4 is included with macOS releases 10.4through 10.14 and is also available from ActiveState. Aqua Carbon variantsof Tk 8.5 had been available as an ActiveState Community Download priorto ActiveTcl 8.5.9. As of 8.5.13, the Tk project no longer supportsCarbon builds of Tk 8.5. 32-bit-only Python installers downloadablefrom this website for older Python releases were linked with Aqua CarbonTk 8.4.
- X11 Tk
- The traditional platform-independent UNIX Tk implementation whichrequires an X11 server, such as the Apple X11.app available as anoptional component in older macOS releases or from third-partydistributors. 64-bit and32-bit binaries can be built. While the Python installers downloadablefrom this website do not support X11 Tk, other distributors ofPython for macOS may do so.
built-in 8.6.8
As of Python 3.7.0, 3.6.8, and 2.7.16, all current Python installers for macOSdownloadable from python.org supplytheir own private copies of Tcl/Tk 8.6.8. They do not look for or use anythird-party or system copies of Tcl/Tk. This is an Aqua Cocoa Tk.
ActiveTcl 8.5.18.0
ActiveState provides binary distributions of Tcl/Tk which are upward compatiblewith and generally more up-to-date than those provided by Apple in macOSreleases. This version of Tcl/Tk includes fixes for some critical problemsthat you may encounter using tkinter or IDLE (see Apple 8.5.9 below).You can download an installer for this release fromthe ActiveState web site.Note that ActiveState Community Edition binaries are not open source andare covered by an ActiveState license. You should read the licensebefore downloading to verify that your usage complies with its terms of use.As of Python 3.7.0, 3.6.8, and 2.7.16, no current Python installers for macOSdownloadable from python.org make use of this or any other external versionof Tcl/Tk.
![Download Download](/uploads/1/2/6/7/126707478/479045885.jpg)
This is an Aqua Cocoa Tk.
Apple 8.5.9
This release is included in macOS 10.7 through at least macOS 10.14.As of this writing,there are at least two known issues with Tk 8.5.9 thatare present in Apple 8.5.9 Tk but fixed in more recent upstream 8.5 releases.The more serious problem is an immediate crash in Tkwhen entering a composition character, like Option-u on a US keyboard.(This problem is documented asTk bug 2907388.)There is also the more general problem of input manager support for compositecharacters(Tk bug 3205153)which has also been fixed in more recent Tcl/Tk 8.5 releases.You can avoid these problems by using a current python.org installeror by using a third-partydistribution of Python that does not use Apple 8.5.9 Tk.This is an Aqua Cocoa Tk.
Apple 8.5.7
Mac Install Tkinter
This release is included in macOS 10.6. IDLE is known to hang or crashwhen used with the Apple 8.5.7 included in all versions of macOS 10.6.x.Because of this,we strongly recommend that you do not attempt to use Tkinter or IDLE withthe Apple-supplied Python 2.6.1 in 10.6. Instead, install a newer version ofPython that supports a newer version of Tk.This is an Aqua Cocoa Tk.
Note
While Tcl and Tk areseparate frameworks and libraries, they are closely related and arenormally installed or updated simultaneously. You should notattempt to mix-and-match Tcl and Tk versions. References toa specific version of Tk assume the corresponding version ofTcl is installed as well.
The Python for macOS installers downloaded from this website dynamicallylink at runtime to Tcl/Tk macOS frameworks. The Tcl/Tk major version isdetermined when the installer is created and cannot be overridden.All current python.org installers for Python 3.7.x, 3.6.x,and 2.7.x link to their own built-in Tcl/Tk 8.6 frameworks and do not useexternal Tcl/Tk frameworks so the rest of this section only applies tonon-current releases and, as such, no longer supported.
The Python 64-bit/32-bit macOS installers for Python 3.6.x andand 2.7.x dynamically link to Tcl/Tk 8.5 frameworks.The dynamically linking occurs when tkinter (Python 3)or Tkinter (Python 2) is first imported (specifically, the internal_tkinter C extension module). By default, the macOS dynamic linkerlooks first in /Library/Frameworks for Tcl and Tk frameworks withthe proper major version. This is the standard location for third-partyor built from source frameworks, including the ActiveTcl releases.If frameworks of the proper major version are not found there,the dynamic linker looks for the same version in/System/Library/Frameworks, the location for Apple-suppliedframeworks shipped with macOS. (Note, you should normally not modifyor delete files in /System/Library.)
As is common on macOS, the installed Pythons and the Tcl and Tkframeworks are built to run on multiple CPU architectures (universalbinaries) and across multiple macOS levels (minimum deploymenttarget). For Python to be able to dynamically link with a particularTcl and Tk version, the available architectures in the Tcl/Tk frameworksmust include the architecture that Python is running in and theirminimum deployment target should be no greater than that of Python.
Tkinter Download Windows 10
- 2020-08-17 - updated for 3.7.9
- 2020-07-20 - updated for 3.8.5
- 2020-06-27 - updated for 3.7.8
- 2020-05-14 - updated for 3.8.3
- 2020-03-10 - updated for 3.8.2 and 3.7.7
- 2019-12-19 - updated for 3.8.1, 3.7.6, and 2.7.17
- 2019-10-15 - updated for 3.8.0, 3.7.5, and macOS 10.15
- 2019-07-08 - updated for 3.7.4; 3.6.x is now security-fix-only
- 2019-03-25 - updated for 3.7.3
- 2019-03-03 - updated for 2.7.16
- 2018-12-24 - updated for 3.7.2 and 3.6.8
- 2018-10-20 - updated for 3.7.1, 3.6.7, and macOS 10.14
- 2018-06-27 - updated for 3.7.0 and 3.6.6
- 2018-05-30 - updated for 3.7.0b5
- 2018-05-02 - updated for 3.7.0b4 and 2.7.15; removed 32-bit-only refs
- 2018-03-29 - updated for 3.7.0b3 and 3.6.5
- 2018-02-28 - updated for 3.7.0b2
- 2018-01-31 - updated for 3.7.0b1 and 3.6.4
- 2017-10-03 - updated for 3.6.3 and macOS 10.13
- 2017-09-16 - updated for 2.7.14; removed 3.5.x
- 2017-07-17 - updated for 3.6.2
- 2017-03-21 - updated for 3.6.1 and (belatedly) 3.5.3
- 2016-12-23 - updated for 3.6.0
- 2016-12-17 - updated for 2.7.13
- 2016-09-23 - updated for macOS 10.12
- 2016-07-31 - updated for 3.5.2 and 2.7.12; removed 3.4.x
- 2015-12-20 - updated for 3.4.4
- 2015-12-06 - updated for 3.5.1, 2.7.11, and macOS 10.11
- 2015-09-13 - updated for 3.5.0
- 2015-05-23 - updated for 2.7.10 and ActiveTcl 8.5.18.0
- 2015-02-23 - updated for 3.4.3
- 2014-12-10 - updated for 2.7.9 and ActiveTcl 8.5.17.0
- 2014-10-16 - updated for macOS 10.10
- 2014-10-06 - updated for 3.4.2 and ActiveTcl 8.5.16.0
- 2014-09-22 - updated for 3.4.2rc1
- 2014-07-01 - updated for 2.7.8
- 2014-06-01 - updated for 2.7.7; removed 2.7.6 and 3.3.5
- 2014-05-18 - updated for 3.4.1 and 2.7.7rc1
- 2014-03-16 - updated for 3.4.0 and 3.3.5
- 2014-02-10 - updated for 3.3.4 and 3.4.0rc1
- 2014-01-05 - updated for 3.4.0b2
- 2013-11-24 - clarify that the ActiveState website still refers to 8.5.15.0
- 2013-11-24 - removed built-in for 3.4.0b1, removed 3.3.2 and 2.7.5
- 2013-11-10 - ActiveTcl 8.5.15.1; removed built-in for 3.3.3rc2 and 2.7.6.
- 2013-10-27 - updated for 3.3.3rc1 and 2.7.6rc1 and their built-in 8.5.15.
- 2013-10-24 - updated for macOS 10.9 and ActiveTcl 8.5.15, removed 3.2.5.
- 2013-10-20 - updated for 3.4.0a4 and its built-in 8.5.15.
- 2013-09-29 - updated for 3.4.0a3
- 2013-09-09 - updated for 3.4.0a2 and its built-in 8.5.14.
- 2013-08-03 - updated for 3.4.0a1 and ActiveTcl 8.4.20
- 2013-05-18 - updated for ActiveTcl 8.5.14
- 2013-05-15 - updated for 3.3.2, 2.7.5, and 3.2.5
- 2013-04-06 - updated for 3.3.1, 2.7.4, and 3.2.4
- 2012-12-26 - updated for ActiveTcl 8.5.13 and Issue 15853 patch installer
- 2012-09-29 - updated for 3.3.0 final and reverted to ActiveTcl 8.5.11.1
- 2012-08-02 - updated for ActiveTcl 8.5.12
- 2012-07-28 - updated for macOS 10.8
- 2012-04-11 - updated for 3.2.3 final and 2.7.3 final
- 2012-03-18 - updated for 3.2.3rc2 and 2.7.3rc2
- 2012-03-04 - updated for ActiveTcl 8.5.11.1, 3.2.3rc1, 2.7.3rc1, removed 3.1.4
- 2011-11-12 - updated for ActiveTcl 8.5.11
- 2011-09-04 - updated for 3.2.2 final
- 2011-07-21 - updated for macOS 10.7 and ActiveTcl 8.5.10.1
- 2011-07-09 - updated for 3.2.1 final and ActiveTcl 8.5.10
- 2011-06-12 - updated for 2.7.2 final and 3.1.4 final
- 2011-05-30 - updated for 3.2.1rc, 2.7.2rc, and 3.1.4rc
- 2011-03-08 - add warnings and include details on how Python links with Tcl/Tk releases
- 2011-02-20 - updated for 3.2 final
- 2011-01-31 draft 1 - preliminary info for 3.2rc2
- 2011-01-14 draft 0