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Command not found after pip install spliceai

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
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updated by smisek • smisek • written by ian_chiquier • ian_chiquier

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

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written by ian_chiquier • ian_chiquier

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

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written by Mensur Dlakic Mensur Dlakic

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.

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written by ian_chiquier • ian_chiquier

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.

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written by h.mon h.mon

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.

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written by ian_chiquier • ian_chiquier

I was having a similar error. I installed spliceai with pip and could run fine in an interactive shell, but I would get 'command not found: spliceai' when submitting a job with qsub. I solved the problem by explicitly giving the path to spliceai (/home/unix/myname/.local/bin/spliceai -I input.vcf -O output.vcf -R ref.fa -A grch38 instead of spliceai -I input.vcf -O output.vcf -R ref.fa -A grch38). Adding the appropriate directory to PATH, as you originally suggested, also solves the problem.

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written by smisek • smisek

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