Won't run in OS 10.9.1 to "Add new species"

[GoogleCodeExporter]

What steps will reproduce the problem?
1.  Open AltAnalyze and begin
2.  Click on Add New Species
3.  receive error and program crashes

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

What version of the product are you using? On what operating system?
Mac OS 10.9.1

Please provide any additional information below.
Console says:
com.apple.launchd.peruser.501: 
([0x0-0x6b96b9].org.pythonmac.unspecified.AltAnalyze[46436]) Exited with code 
255

Original issue reported on code.google.com by c.joel.m...@gmail.com on 10 Jan 2014 at 6:18

[GoogleCodeExporter]

AltAnalyze has not been tested yet on Mac OS 10.9.1, however, we have received 
other reports of incompatibility with this OS. We expect to upgrade at least 
one test machine to this OS in early February in coordination with our IT 
department. 

In the meantime, I recommend either running AltAnalyze from source code and 
installing necessary dependencies described here:
http://code.google.com/p/altanalyze/wiki/StandAloneDependencies 

Alternatively, you can install a desktop virtual app, such as VirtualBox with 
Windows or Ubuntu 12.04 and run the compiled AltAnalyze version there.

Original comment by nsalomo...@gmail.com on 13 Jan 2014 at 9:05

[GoogleCodeExporter]

Thanks for the reply.  I tried running it through a virtualbox Linux Ubuntu 
12.04 installation on my Mac, and have the same issue.  Originally the program 
worked, but wouldn't "Add New Species".  After I chose a species from the 
server, the program did allow me to attempt to "Add New Species" but crashed 
after I gave the species name and now won't run at all.  Now when I click on 
"begin analysis" it crashes.

Please help.

Original comment by c.joel.m...@gmail.com on 15 Jan 2014 at 2:42

[GoogleCodeExporter]

Does it work if you just select a species to download? What species are you 
trying to add? What kind of data is this?

The species addition is only useful if you want to manually create a species 
database outside of AltAnalyze, and really only that is useful for non-splicing 
analyses. My recommendation is that if AltAnalyze works fine on Mac or Ubuntu 
with a downloaded species and if you have gene/metabolite/proteomics data for a 
non-supported species, just download the Zea Mays database (smallest in size), 
pick "Other" as your system and any of the ID systems shown below and proceed 
with your analysis. This will give you all of the basic statistical and 
comparison analyses, including MarkerFinder, PCA, hierarchical clustering and 
other QC, but won't add any annotations to your data. 

Original comment by nsalomo...@gmail.com on 15 Jan 2014 at 3:09

[GoogleCodeExporter]

My goal is to run splicing analysis on RNA-seq data from the purple sea urchin 
(S. purpuratus), that has a genome and gff annotation files from cufflinks / 
publications.  If it's not possible to perform splicing analysis with a "New 
Species" then I will need to look elsewhere for another application, correct?

Original comment by c.joel.m...@gmail.com on 15 Jan 2014 at 3:22

[GoogleCodeExporter]

My goal is to run splicing analysis on RNA-seq data from the purple sea urchin 
(S. purpuratus), that has a genome and gff annotation files from cufflinks / 
publications.  If it's not possible to perform splicing analysis with a "New 
Species" then I will need to look elsewhere for another application, correct?

Original comment by c.joel.m...@gmail.com on 15 Jan 2014 at 3:59

[GoogleCodeExporter]

Although it has been on our action item list add support for the Ensembl 
bacterial, metazoan, etc. websites, which will just require some tweaking to 
our update code to allow for this different build sites, we haven't yet. 

If you are python friendly I can tell you how to do this on a species by 
species basis, but otherwise it won't be available for the new few months at 
least.

Best,
Nathan

Original comment by nsalomo...@gmail.com on 15 Jan 2014 at 6:22