"CIRIquant" is a Python package for detecting Circular RNA. I installed "CIRIquant" through the below command in terminal:

pip install CIRIquant

My Linux distribution is Ubuntu 16.04 and my python version is Python 2.7.12. After installing, I got the below message: “Installing collected packages: numpy, scipy, scikit-learn, pysam, PyYAML, argparse, numexpr, CIRIquant Successfully installed CIRIquant-1.1.2 PyYAML-5.1.1 argparse-1.2.1 numexpr-2.6.9 numpy-1.16.4 pysam-0.15.2 scikit-learn-0.20.3 scipy-1.2.2”

So, When I call CIRIquant for running its function in Terminal, I got the below message in Terminal:

CIRIquant: command not found

Now, I don't know what is my problem? I appreciate it if anybody shares his/her comment with me. Best,

  • 1
    $\begingroup$ did you activate your virtualenv environment? source ./venv/bin/activate $\endgroup$
    – zorbax
    Oct 12, 2021 at 12:34
  • 1
    $\begingroup$ Dear @zorbax, No. I didn't activate virtualenv. is it necessary? because I didn't install CIRIquant from the source code. could you please guide me? $\endgroup$
    – Mohammad
    Oct 12, 2021 at 13:46

1 Answer 1


When I try this as a regular user on our Ubuntu 16 LTS system, I end up with ~/.local/bin/CIRIquant from the pip install, so maybe just add that directory to your path:

$ export PATH="$HOME/.local/bin:$PATH"
$ CIRIquant -h
usage: CIRIquant [-h] [--config FILE] [-1 MATE1] [-2 MATE2] [-o DIR]
                 [-p PREFIX] [-t INT] [-a INT] [-l INT] [-v] [--version]
                 [-e LOG] [--bed FILE] [--circ FILE] [--tool TOOL]
                 [--RNaseR FILE] [--bam BAM] [--no-gene]
  • $\begingroup$ Dear @Jesse I set export PATH="$HOME/.local/bin:$PATH" and I could run CIRIquant -h but now when I run e.g: ls then the system give me below comment: "ls: command not found" and error related to PATH environment variable $\endgroup$
    – Mohammad
    Oct 13, 2021 at 11:45
  • 1
    $\begingroup$ Make sure you kept your old $PATH as part of the new string, rather than having only the new path (which is what that sounds like to me). You can echo $PATH before and after the change to check it. You should still see things like /usr/bin in there afterward. $\endgroup$
    – Jesse
    Oct 13, 2021 at 13:05

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