Question: Issue installing gprofiler (following biostar handbook)
0
gravatar for ccc
6 weeks ago by
ccc20
ccc20 wrote:

I'm following the gprofiler command line installer from the book, and I run

pip install gprofiler-official

And it says success. But then I run

gprofiler_cli.py --help

And it says "command not found". I found where gprofiler was pip installed, so I know it's here, although I didn't find gprofiler_cli.py, I just found gprofiler.py. But trying to run that didn't work either (and also says that file doesn't exist). Any idea what is going on?

software error • 170 views
ADD COMMENTlink modified 6 weeks ago by GenoMax96k • written 6 weeks ago by ccc20
1

I have opened an issue here:

https://github.com/biostars/biostar-handbook-issues/issues/138

to investigate this error, once solved we will indicate the resolution as an answer here

ADD REPLYlink written 6 weeks ago by Istvan Albert ♦♦ 86k

Not sure if this applies in your case: How to run g:profiler on macOS

Tagging: Istvan Albert

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by GenoMax96k

Perfect, that did work - the answerer uku.raudvere states that "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."

does that mean there is no up to date command line tool as of 17 months ago, or am I misreading that? Is there any update to this situation?

edit: thought I'd ask here, as wasn't sure if commenting on an ancient thread is considered bad taste here!

ADD REPLYlink modified 6 weeks ago by Istvan Albert ♦♦ 86k • written 6 weeks ago by ccc20
1

Asking here is fine. I tagged Istvan Albert who is author of biostar handbook. He may need to revise this part in the book.

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by GenoMax96k
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