Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-10-13T11:45:33.267Z
Answers.Text: 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
Answers.UserDisplayName: Mohammad
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-10-13T13:05:07.160Z
Answers.Text: 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.
Answers.UserDisplayName: Jesse
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-10-12T15:30:59.983Z
Answers.LastActivityDate: 2021-10-12T15:30:59.983Z
Answers.UserDisplayName: Jesse
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-10-12T12:34:46.050Z
Comments.Text: did you activate your virtualenv environment? `source ./venv/bin/activate`
Comments.UserDisplayName: zorbax
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-10-12T13:46:39.100Z
Comments.Text: 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?
Comments.UserDisplayName: Mohammad
Tags: <rna-seq><python>
Title: Error to running "CIRIquant" function in CIRIquant package at python Language
ThreadText: # Error to running "CIRIquant" function in CIRIquant package at python Language
  
  (Asked by: username_0 on 2021-10-12)
  
  "[CIRIquant](https://ciri-cookbook.readthedocs.io/en/latest/CIRIquant_1_installation.html)" 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 @username_1, 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 @username_2 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.  
  
  ---
  
  