Re: AltAnalyze User Group Trouble for running AltAnalyze

[Nathan Salomonis]

Hi Luz,

We have encountered this issue on different machines with different operating systems as wx is finiky. We hope to fix when adding support for the latest Mac processors. I would recommend looking at the PDF files that accompany the primary AltAnalyze results and the online tutorials (including videos) which should walk you through the results, as this can be accomplished through local PDF viewers, Excel and AltAnalyze itself.

Happy to help interpret any results.

Best,

Nathan

On Sep 20, 2022, at 8:20 AM, Luz E Cabrera <luzen...@gmail.com> wrote:

Hi,

I encounter the same issue with MacOS... "depedency not met for: wx". 

Has any solution been found for this?

Kind regards,

Luz Cabrera

On Friday, March 22, 2019 at 12:14:07 PM UTC+2 david....@gmail.com wrote:

Hi Nathan, thank you for your fast answer ! 

However, I still get some trouble when I try this pre-compiled version...

I can't even download the genomes this time...

Last login: Fri Mar 22 10:45:21 on ttys000
(base) C07NP206G1J2:~ david.benacom$ /Applications/AltAnalyze/AltAnalyze.app/Contents/MacOS/AltAnalyze ; exit;

AltAnalyze depedency not met for: wx
...The AltAnalyze Results Viewer requires wx

WARNING!!!! Some dependencies are not currently met.
This may impact AltAnalyze's performance

Traceback (most recent call last):
  File "/Applications/AltAnalyze/AltAnalyze.app/Contents/Resources/__boot__.py", line 112, in <module>
    _run()
  File "/Applications/AltAnalyze/AltAnalyze.app/Contents/Resources/__boot__.py", line 82, in _run
    exec(compile(source, path, 'exec'), globals(), globals())
  File "/Applications/AltAnalyze/AltAnalyze.app/Contents/Resources/AltAnalyze.py", line 8560, in <module>
    if use_Tkinter == 'yes': AltAnalyzeSetup(skip_intro)
  File "/Applications/AltAnalyze/AltAnalyze.app/Contents/Resources/AltAnalyze.py", line 5144, in AltAnalyzeSetup
    expr_var, alt_var, additional_var, goelite_var, exp_file_location_db = UI.getUserParameters(skip_intro,Multi=mlp)
  File "UI.pyc", line 4993, in getUserParameters
  File "UI.pyc", line 4685, in addOnlineSpeciesDatabases
UnboundLocalError: local variable 'sc' referenced before assignment
2019-03-22 11:11:34.539 AltAnalyze[42113:2012030] AltAnalyze Error
logout
Saving session...
...copying shared history...
...saving history...truncating history files...
...completed.
Deleting expired sessions...77 completed.

[Opération terminée]

Le ven. 8 mars 2019 à 22:35, Nathan Salomonis <nsalo...@gmail.com> a écrit :

Hi David,

AltAnalyze has a number of Python dependencies which are not installed by default in anaconda. The warnings you are getting relate to missing python packages. It is for this reason we provide two alternative ways to run AltAnalyze on a Mac:

1) The pre-compiled version as Mac and Windows binaries:

http://altanalyze.org/downloads/AltAnalyze_v.2.1.2_OSX-64bit.dmg

2) PyPI installer: pip install altanalyze (Python 2.7 only)

The latter will not properly bring down iGraph which is a pain to get installed correctly, hence, I would try 1. If you want to keep with the anaconda solution, then try the following:

pip install umap-learn, nimfa, numba, community, annoy, networkx, R 3+, fastcluster, pillow, pysam, requests, pandas, patsy, lxml, python-igraph, cairo

For iGraph, try installing with:

https://igraph.org/nightly/get/python-osx/python_igraph-0.7.0-py2.7-macosx10.8.dmg

Best,

Nathan

On Fri, Mar 8, 2019 at 7:57 AM <david....@gmail.com> wrote:

Hello, and thank you for your tremendous work !

I want to use your program to analyze the Alternative splicing events in RNA-seq data, between to conditions (Homo vs Hetero)

I have the FASTQ files, and the BAM/BAI

I understood that the FASTQ were better, so I wanted to run a complete analysis, but I got the following error (see attached). I have some results at the end, but I cannot be confident knowing the number of errors that seems to happend.

I'm kind of new to programming, so there may be something I did completely wrong !

I have AltAnalyze on a virtual environnement of Anaconda, with python 2.7; I tried to have all the dependencies needed, but some for instance cairo I can't find...

I hope you may help me. Thanks a lot...

Cheers

David

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