Answers.Body: <p>If you're in the RepeatScout directory you need to execute the Perl script with a <code>./</code> prefix, like so.</p>
  
  <pre><code>cat od_1000_repeats.fa | ./filter-stage-1.prl &gt; od_1000_repeats_filt1.fa
  </code></pre>
  
  <p>If you're not in the RepeatScout directory, you need to provide the full relative or absolute path when executing the script. Alternatively, you can put the RepeatScout directory in your <code>$PATH</code> environmental variable.</p>
  
  <p>These are all standard UNIX/Linux concepts that many bioinformaticians take for granted, for better and for worse. If you're lost in all the terminology, a crash course in UNIX basics is probably where you would want to start.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-05-01T17:18:29.910Z
Answers.Text: I installed repeatscout on my PC, I created the Repeatscout directory and It worked without errors. The problem is that it can't execute a file larger more than 800 mb in a 16 gb ram of my pc. So I had to use the cluster but I don't know where is the Repeatscout directory.(If I put "locate Repeatscout" I don't find it). I would to find the path to check if all the programs are correctly installed..
Answers.UserDisplayName: jonny
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-05-01T18:12:21.600Z
Answers.Text: It sounds like you need to get some help from your system administrator.
Answers.UserDisplayName: Daniel Standage
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-05-01T15:50:29.220Z
Answers.LastActivityDate: 2019-05-01T15:50:29.220Z
Answers.UserDisplayName: Daniel Standage
Body: <p>I've installed Repeatscout from <a href="https://bix.ucsd.edu/repeatscout/" rel="nofollow noreferrer">https://bix.ucsd.edu/repeatscout/</a>.
  I've also installed TRF and nseg required by the program. 
  I followed the steps:</p>
  
  <pre><code>build_lmer_table -l 16 -sequence ~/file_fasta/od_1000.fa -freq od_1000.freq
  </code></pre>
  
  <pre><code> RepeatScout -sequence od_1000.fa -output od_1000_repeats.fa -freq od_1000.freq -l 16
  </code></pre>
  
  <p>and the I put this command:</p>
  
  <pre><code>cat od_1000_repeats.fa| filter-stage-1.prl &gt;od_1000_repeats_filt1.fa 
  </code></pre>
  
  <p>but this message appears:</p>
  
  <pre><code>bash: filter-stage-1.prl: command not found...
  </code></pre>
  
  <p>Why? It is all correctly installed, I can't understand the problem</p>
  
Tags: <software-installation>
Title: Repeatscout installation problem
ThreadText: # Repeatscout installation problem
  
  (Asked by: username_0 on 2019-05-01)
  
  I've installed Repeatscout from <https://bix.ucsd.edu/repeatscout/>.
  I've also installed TRF and nseg required by the program.
  I followed the steps:
  
  ```
  build_lmer_table -l 16 -sequence ~/file_fasta/od_1000.fa -freq od_1000.freq
  
  ```
  
  ```
   RepeatScout -sequence od_1000.fa -output od_1000_repeats.fa -freq od_1000.freq -l 16
  
  ```
  
  and the I put this command:
  
  ```
  cat od_1000_repeats.fa| filter-stage-1.prl >od_1000_repeats_filt1.fa 
  
  ```
  
  but this message appears:
  
  ```
  bash: filter-stage-1.prl: command not found...
  
  ```
  
  Why? It is all correctly installed, I can't understand the problem
  
  **Tags:** software-installation
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-05-01. Score: 2 | Accepted answer
  
  If you're in the RepeatScout directory you need to execute the Perl script with a `./` prefix, like so.
  
  ```
  cat od_1000_repeats.fa | ./filter-stage-1.prl > od_1000_repeats_filt1.fa
  
  ```
  
  If you're not in the RepeatScout directory, you need to provide the full relative or absolute path when executing the script. Alternatively, you can put the RepeatScout directory in your `$PATH` environmental variable.
  
  These are all standard UNIX/Linux concepts that many bioinformaticians take for granted, for better and for worse. If you're lost in all the terminology, a crash course in UNIX basics is probably where you would want to start.
  
  > **Comments:**
  > **username_0**: I installed repeatscout on my PC, I created the Repeatscout directory and It worked without errors. The problem is that it can't execute a file larger more than 800 mb in a 16 gb ram of my pc. So I had to use the cluster but I don't know where is the Repeatscout directory.(If I put "locate Repeatscout" I don't find it). I would to find the path to check if all the programs are correctly installed..  
  > **username_1**: It sounds like you need to get some help from your system administrator.  
  
  ---
  
  