Cannot open altanalyze on mac

[GoogleCodeExporter]

What steps will reproduce the problem?
1. When I click on the altAnalyze icon, after downloading to my applications 
folder, I get the message "Altanalyze has encountered a fatal error, and will 
no termiate."
2.
3.

What is the expected output? What do you see instead?

What version of the product are you using? On what operating system? all 
versions I try. mac os X version 10.5.8

Please provide any additional information below.

Original issue reported on code.google.com by johnanth...@gmail.com on 3 Oct 2011 at 6:12

[GoogleCodeExporter]

Although the compiled AltAnalyze for Mac run fine on Mac OS X 10.6 and above, 
stand-alone mac version of AltAnalyze will run on the operating system that it 
was built upon. This is because AltAnalyze is compiled with py2app which will 
store OS dependent files for running AltAnalyze. There are three possible fixes 
to this:

1) If running Mac OS X 10.5 and below, download and run the Python source code 
version (http://code.google.com/p/altanalyze/wiki/RunningSourceCode), which 
runs identical to the compiled version. Mac OS X has python installed already 
by default.
2) Compile AltAnalyze from source code. This is only useful if you want to 
distribute to other Mac OX 10.5 and below users. You can do this by installing 
py2app (e.g., using easy install after setuptools).
3) AltAnalyze.org to distribute binaries for different flavors of the Mac OS X

The third options currently is too difficult, since it requires us to maintain 
multiple computers with different Mac operating systems. Alternatively, we will 
consider distributing binaries built by users (after extensive evaluation).

Original comment by nsalomo...@gmail.com on 3 Oct 2011 at 11:35

[nsalomonis]

I am re-opening this issue as running AltAnalyze on a Mac for the first time is presenting with a number of new issues:

1) In Mac OS X 10.4, a critical vulnerability prevents running the GUI version of the software (pre-combined by AltAnalyze or source-code run via the GUI). The software can only by run by command-line mode or the software may prevent you to run. If this is so, you must comment-out the restriction to run posix 10.4 in the AltAnalyze.py module. Running the GUI will cause the operating system to crash (OS incompatibility with Tkinter/TCL backends).

2) Mac OS X will not allow the user to run the software automatically by default (Mac OS X 10.3 and greater). This issue spawns from the AltAnalyze developer team not embedded the Apple Developer certificate with the pre-compiled OS version. There are two solutions to this issue:

• Open System Preferences > Security and Privacy > General. See the option to allow AltAnalyze to be run. Following this, right click on one of the two green AltAnalyze icons to open (will require the user to acknowledge they are opening a program downloaded from the internet). The same issue may present when analyzing FASTQ files, for the same issue with the Kallisto pre-compiled binary. For more on this issue, see: https://youtu.be/DHKIJKWr3ag
• Run AltAnalyze from source-code or PyPI installation (pip install altanalyze).

A long-term solution for these problems are in the works.