Incomplete Install

[sandyl27]

I installed rnalysis by following the installation instructions but it didn't install all of the files. I am on MacOS Ventura and I am using python 3.9

[GuyTeichman]

Hi, What command exactly did you use? What feedback did you get after typing the terminal command?

My guess would be that you had a previous version of RNAlysis installed on your system, and you would need to upgrade the existing installation instead of installing a new one.

The command would look like so for the basic version: pip install --upgrade RNAlysis

And like so for the full version: pip install --upgrade RNAlysis[all]

Please let me know if that works. Best, Guy.

[sandyl27]

I got it figured out. Thank you!

But now I'm getting this error

Traceback (most recent call last): File "rnalysis/utils/differential_expression.py", line 81, in install_deseq2 File "rnalysis/utils/io.py", line 1373, in run_r_script AssertionError: R script failed to execute (return code 2).

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "rnalysis/gui/gui.py", line 3637, in finish_generic_job File "rnalysis/gui/gui_widgets.py", line 291, in run File "rnalysis/filtering.py", line 2721, in differential_expression_deseq2 File "rnalysis/utils/differential_expression.py", line 123, in run_deseq2_analysis File "rnalysis/utils/differential_expression.py", line 83, in install_deseq2 AssertionError: Failed to install DESeq2. Please make sure you have write premission to R's library folder, or try to install DESeq2 manually.

But I have DESeq2 installed already

[GuyTeichman]

Hi, could you please post the output of the R script, which appears in the RNAlysis log box at the bottom of you screen?

[sandyl27]

The path to that file on my computer is /private/var/folders/l0/05jlfmt17hn03llpf45gqw3h0000gn/T/_MEIe6vs4z/rnalysis/data_files/r_templates/deseq2_install.R

[GuyTeichman]

Hi, Thanks for the bug report. I think I figured out what the issue is - there appears to be a problem with pointing RNAlysis to the R script which installs DESeq2. The issue should be fixed in the next minor release of RNAlysis (3.6.0), which will be released in a week or two.

Unfortunately, the only workaround I can suggest in the meantine is to run RNAlysis on a computer with a different operating system (Windows or Linux), or to run your DESeq2 analysis manually through R.

Thanks and sorry for the inconvenience, Guy.