Question: Command not found after pip install spliceai
0
gravatar for ian_chiquier
24 days ago by
ian_chiquier0 wrote:

Hi everyone, I used pip install to install spliceai, but then when I try to use commands like spliceai at the command line it says command not found. I believe I need to move something to my "PATH", but I am pretty unfamiliar with this and am not sure how it works (also new to using pip install) so would appreciate any advice.

Thank you!

software error • 108 views
ADD COMMENTlink written 24 days ago by ian_chiquier0

I'd suggest installing via Conda

ADD REPLYlink written 24 days ago by andrew.j.skelton736.0k

Hey I installed Miniconda2, but when I try to do conda install -c bioconda spliceai it says zsh: command not found: conda

ADD REPLYlink written 24 days ago by ian_chiquier0

It is possible that you need to log out and back in for the installation to work. Or try typing rehash on command line.

ADD REPLYlink written 24 days ago by Mensur Dlakic7.1k

I think it said at one point that it installed successfully - I just think it isn't in my PATH or something (from what I read about online regarding this type of issue). I just don't know how to navigate my files in a way that moves the installed commands on to my PATH so that they may be executed.

ADD REPLYlink written 24 days ago by ian_chiquier0

Please copy and paste the commands you used, and the error message.

Did you (pip) install TensorFlow as well? It is a requirement, but it isn't installed automatically.

ADD REPLYlink written 24 days ago by h.mon31k

ianchiquier@Ians-MBP-2 % cat current_input.vcf | spliceai -R genome.fa -A grch38 > novel_output.vcf zsh: command not found: spliceai

And I just did pip install TensorFlow and still get the same error.

ADD REPLYlink written 24 days ago by ian_chiquier0
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