How to run g:profiler on macOS

Question

[michael.flower.14]

I'm new to bioinformatics, and am learning to use g:profiler. I'm using a terminal on a mac. The advice I got was:

Install the client.

pip install gprofiler-official #this works fine, and says "Requirement already satisfied"

Get help on the client parameters.

gprofiler_cli.py --help

the output I get is:

$ gprofiler_cli.py --help -bash: gprofiler_cli.py: command not found (base)

Example run from the documentation.

gprofiler_cli.py -o scerevisiae "swi4 swi6"

the output I get is:

$ gprofiler_cli.py -o scerevisiae "swi4 swi6" -bash: gprofiler_cli.py: command not found (base)

I'd be grateful for any help as I'm stuck, despite reading around the internet Thanks!

Answer 1

[uku.raudvere]

Hi!

g:Profiler had a major update earlier this year that deprecated the use of gprofiler_cli.py.

To make gprofiler_cli.py work again, I'd recommend uninstalling gprofiler-official and reinstalling the 0.3.5 version.

pip uninstall gprofiler-official

pip install gprofiler-official==0.3.5

The caveat is that the data behind gprofiler-official version 0.3.5 is not getting updates anymore. Generally we recommend using the latest version of gprofiler-official as a python client or the gprofiler2 R package (https://CRAN.R-project.org/package=gprofiler2). We don't currently have a command line tool for accessing g:Profiler.

[michael.flower.14]

Brilliant, that's worked perfectly! Thanks!