<p>When I try this as a regular user on our Ubuntu 16 LTS system, I end up with <code>~/.local/bin/CIRIquant</code> from the pip install, so maybe just add that directory to your path:</p>
<pre><code>$ export PATH=&quot;$HOME/.local/bin:$PATH&quot;
$ 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]
</code></pre>

CC BY-SA 4.0
2021-10-13T11:45:33.267Z
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
Mohammad
CC BY-SA 4.0
2021-10-13T13:05:07.160Z
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.
Jesse
CC BY-SA 4.0
2021-10-12T15:30:59.983Z
2021-10-12T15:30:59.983Z
Jesse
<p>&quot;<a href="https://ciri-cookbook.readthedocs.io/en/latest/CIRIquant_1_installation.html" rel="nofollow noreferrer">CIRIquant</a>&quot; is a Python package for detecting Circular RNA. I installed &quot;CIRIquant&quot; through the below command in terminal:</p>
<blockquote>
<p>pip install CIRIquant</p>
</blockquote>
<p>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”</p>
<p>So, When I call CIRIquant for running its function in Terminal, I got the below message in Terminal:</p>
<pre><code>CIRIquant: command not found
</code></pre>
<p>Now, I don't know what is my problem?
I appreciate it if anybody shares his/her comment with me.
Best,</p>

CC BY-SA 4.0
2021-10-12T12:34:46.050Z
did you activate your virtualenv environment? `source ./venv/bin/activate`
zorbax
CC BY-SA 4.0
2021-10-12T13:46:39.100Z
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?
Mohammad
<rna-seq><python>
Error to running "CIRIquant" function in CIRIquant package at python Language
# Error to running "CIRIquant" function in CIRIquant package at python Language

(Asked by: username_0 on 2021-10-12)

"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,

**Tags:** rna-seq, python
> **Comments:**
> **username_1**: did you activate your virtualenv environment? `source ./venv/bin/activate`  
> **username_0**: 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?  

---

## 1 answers

### Answer by username_2 on 2021-10-12. Score: 3 | Accepted answer

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]

> **Comments:**
> **username_0**: 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  
> **username_2**: 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.  

---

