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3.2 years ago
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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?
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
Not sure if this applies in your case: How to run g:profiler on macOS
Tagging: Istvan Albert
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!
Asking here is fine. I tagged Istvan Albert who is author of biostar handbook. He may need to revise this part in the book.