text: user6948: I am trying to analyze my RNAseq reads for defective genomes and I use this program (http://www.di-tector.cyame.eu/) that is suggested by Beauclair et al (https://pubmed.ncbi.nlm.nih.gov/30012569/)  for that.
  After downloading a .py script and running it with the following command: 
  sudo python3 DI-tector_06.py /mnt/e/nastya/SLX066-02/sequence.fasta /mnt/e/nastya/SLX066-02/B-dVMV-RIG-1/B-dVMV-RIG-1_ACAGTG_L008_R1_001.rc.fastq.gz 
  
  It says at the beginning that 
  =================================
  Program: DI-tector
  Version: 0.6 - Last modified 25/05/2018
  =================================
  Requirement: (must be in your $PATH)
  -bwa
  -samtools
  
  Optional: (must be in your $PATH)
  -bedtools
  
  I have tried to install bwa using:
  sudo apt-get update -y
  sudo apt-get install -y bwa
  
  and samtools using 
  cd /usr/local/bin
  sudo wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2
  sudo tar -vxjf samtools-1.9.tar.bz2
  cd samtools-1.9
  sudo make
  
  I did not get exactly what does that mean: (must be in your $PATH) but I have searched here and there and discovered that it might mean /usr/local/bin
  The program starts and, after some calculations it gives me the following error:
  Input file:               /mnt/e/nastya/SLX066-02/B-dVMV-RIG-1/B-dVMV-RIG-1_ACAGTG_L008_R1_001.rc.fastq.gz
  Host reference:           None
  Virus reference:          /mnt/e/nastya/SLX066-02/sequence.fasta
  Remove segment:         < 15 nt
  Remove reads with MAPQ: < 25
  Allow InDel. length:    > 1 nt
  
  =================================
  Reading gziped input file...
  =================================
  Number of reads in input file: 18,035,544
  =================================
  
  =================================
  Step 1/5 : Alignment against Viral reference...Filtering...
  =================================
  [E::bwa_idx_load_from_disk] fail to locate the index files
  Traceback (most recent call last):
    File "DI-tector_06.py", line 183, in <module>
      Popen(["samtools", "view", "-Sb", "-F", "4"], stdin=out_file_onVirus, stdout=out_file_Virus).communicate()[0]
    File "/usr/lib/python3.6/subprocess.py", line 709, in __init__
      restore_signals, start_new_session)
    File "/usr/lib/python3.6/subprocess.py", line 1344, in _execute_child
      raise child_exception_type(errno_num, err_msg, err_filename)
  PermissionError: [Errno 13] Permission denied: 'samtools'
  
  I have no idea how samtools must be accessed, I tried sudo command with python3 but it did not work.
  
  user2388: You can run a piece of software by specifying exactly where it is, like /home/usr/software/samtools_1.1.0/samtools
  Or if that location is in your $PATH, you can run it with just samtools.  The software you downloaded needs to run those programs, but there's no way for you to give it the specific path for them; it's going to try and run them with just samtools.  So you need to make sure that will work, by putting their locations in your PATH.
  It is not clear to me that running every command with sudo is wise.  If you don't understand what $PATH is, I'm pretty sure you should not be running everything with sudo.
  
  user3848: The clean way to do this is to make your own bin within your user directory
  cd ~
  mkdir bin
  vi .profile # or vi .profile_bash or for OS X using `csh` or `tcsh` vi .cshrc
  
  For bash (Linux, or OS X) within vi type "i" then type,
  PATH=$PATH:~/bin
  
  or
  PATH=~/bin:$PATH
  
  ... followed by esc key and "wp" enter
  Then enter for csh or tcsh e.g. for OS X
  set path = ($path /Users/username/bin /Users/username/anaconda3/bin)
  
  Same instructions for using vi as for bash. Dump bedtools into any directory (not the desktop) and connect the programs into the bin using ln
  cd ~/progs/bedtools
  ln -si $PWD/prog ~/bin
  
  If you are using csh or tcsh you need to type rehash but bash does this automatically.
  The programs will then be cleaning connect to your $PATH via ln without massive memory usage and visible anywhere within your home space. Its good practice for any Linux / OS X (time gone by UNIX) program or script and whilst you don't need it for this operation as you add more stuff its better.
  
  user7476: you can add a directory to $PATH by executing following command in the terminal:
  export PATH="$HOME/Documents/Software/bbmap:$PATH"
  In this example, all executable commands in the folder bbmap can be executed from any other directory in the terminal.
  So you can install samtools in an appropriate directory and then execute export PATH="$HOME/your/directory:$PATH". Then check if it succeeded by running echo $PATH. This latter command will return a list of directories which are assigned to $PATH and your new directory (where samtools is located) should be included.
  
  user77: echo $PATH will show the directories in your search path. Either copy the samtools executable there or add its location to the $PATH variable. You would be well served with a unix command line course or tutorial.
  
original_text: 6948: <p>I am trying to analyze my RNAseq reads for defective genomes and I use this program (<a href="http://www.di-tector.cyame.eu/" rel="nofollow noreferrer">http://www.di-tector.cyame.eu/</a>) that is suggested by Beauclair et al (<a href="https://pubmed.ncbi.nlm.nih.gov/30012569/" rel="nofollow noreferrer">https://pubmed.ncbi.nlm.nih.gov/30012569/</a>)  for that.</p>
  
  <p>After downloading a .py script and running it with the following command: </p>
  
  <pre><code>sudo python3 DI-tector_06.py /mnt/e/nastya/SLX066-02/sequence.fasta /mnt/e/nastya/SLX066-02/B-dVMV-RIG-1/B-dVMV-RIG-1_ACAGTG_L008_R1_001.rc.fastq.gz 
  </code></pre>
  
  <p>It says at the beginning that </p>
  
  <pre><code>=================================
  Program: DI-tector
  Version: 0.6 - Last modified 25/05/2018
  =================================
  Requirement: (must be in your $PATH)
  -bwa
  -samtools
  
  Optional: (must be in your $PATH)
  -bedtools
  </code></pre>
  
  <p>I have tried to install bwa using:</p>
  
  <pre><code>sudo apt-get update -y
  sudo apt-get install -y bwa
  </code></pre>
  
  <p>and samtools using </p>
  
  <pre><code>cd /usr/local/bin
  sudo wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2
  sudo tar -vxjf samtools-1.9.tar.bz2
  cd samtools-1.9
  sudo make
  </code></pre>
  
  <p>I did not get exactly what does that mean: <strong>(must be in your $PATH)</strong> but I have searched here and there and discovered that it might mean <code>/usr/local/bin</code></p>
  
  <p>The program starts and, after some calculations it gives me the following error:</p>
  
  <pre><code>Input file:               /mnt/e/nastya/SLX066-02/B-dVMV-RIG-1/B-dVMV-RIG-1_ACAGTG_L008_R1_001.rc.fastq.gz
  Host reference:           None
  Virus reference:          /mnt/e/nastya/SLX066-02/sequence.fasta
  Remove segment:         &lt; 15 nt
  Remove reads with MAPQ: &lt; 25
  Allow InDel. length:    &gt; 1 nt
  
  =================================
  Reading gziped input file...
  =================================
  Number of reads in input file: 18,035,544
  =================================
  
  =================================
  Step 1/5 : Alignment against Viral reference...Filtering...
  =================================
  [E::bwa_idx_load_from_disk] fail to locate the index files
  Traceback (most recent call last):
    File "DI-tector_06.py", line 183, in &lt;module&gt;
      Popen(["samtools", "view", "-Sb", "-F", "4"], stdin=out_file_onVirus, stdout=out_file_Virus).communicate()[0]
    File "/usr/lib/python3.6/subprocess.py", line 709, in __init__
      restore_signals, start_new_session)
    File "/usr/lib/python3.6/subprocess.py", line 1344, in _execute_child
      raise child_exception_type(errno_num, err_msg, err_filename)
  PermissionError: [Errno 13] Permission denied: 'samtools'
  </code></pre>
  
  <p>I have no idea how samtools must be accessed, I tried <code>sudo</code> command with python3 but it did not work.</p>
   2388: <p>You can run a piece of software by specifying exactly where it is, like <code>/home/usr/software/samtools_1.1.0/samtools</code></p>
  
  <p>Or if that location is in your $PATH, you can run it with just <code>samtools</code>.  The software you downloaded needs to run those programs, but there's no way for you to give it the specific path for them; it's going to try and run them with just <code>samtools</code>.  So you need to make sure that will work, by putting their locations in your PATH.</p>
  
  <p>It is not clear to me that running every command with sudo is wise.  If you don't understand what $PATH is, I'm pretty sure you should not be running everything with sudo.</p>
   3848: <p>The clean way to do this is to make your own <code>bin</code> within your user directory</p>
  <pre><code>cd ~
  mkdir bin
  vi .profile # or vi .profile_bash or for OS X using `csh` or `tcsh` vi .cshrc
  </code></pre>
  <p>For bash (Linux, or OS X) within vi type &quot;i&quot; then type,</p>
  <pre><code>PATH=$PATH:~/bin
  </code></pre>
  <p>or</p>
  <pre><code>PATH=~/bin:$PATH
  </code></pre>
  <p>... followed by <code>esc</code> key and &quot;wp&quot; <code>enter</code>
  Then enter for <code>csh</code> or <code>tcsh</code> e.g. for OS X</p>
  <pre><code>set path = ($path /Users/username/bin /Users/username/anaconda3/bin)
  </code></pre>
  <p>Same instructions for using <code>vi</code> as for <code>bash</code>. Dump bedtools into any directory (not the desktop) and connect the programs into the bin using <code>ln</code></p>
  <pre><code>cd ~/progs/bedtools
  ln -si $PWD/prog ~/bin
  </code></pre>
  <p>If you are using <code>csh</code> or <code>tcsh</code> you need to type <code>rehash</code> but <code>bash</code> does this automatically.</p>
  <p>The programs will then be cleaning connect to your $PATH via <code>ln</code> without massive memory usage and visible anywhere within your home space. Its good practice for any Linux / OS X (time gone by UNIX) program or script and whilst you don't need it for this operation as you add more stuff its better.</p>
   7476: <p>you can add a directory to <code>$PATH</code> by executing following command in the terminal:</p>
  <p><code>export PATH=&quot;$HOME/Documents/Software/bbmap:$PATH&quot;</code></p>
  <p>In this example, all executable commands in the folder <code>bbmap</code> can be executed from any other directory in the terminal.</p>
  <p>So you can install <code>samtools</code> in an appropriate directory and then execute <code>export PATH=&quot;$HOME/your/directory:$PATH&quot;</code>. Then check if it succeeded by running <code>echo $PATH</code>. This latter command will return a list of directories which are assigned to <code>$PATH</code> and your new directory (where <code>samtools</code> is located) should be included.</p>
   77: <p><code>echo $PATH</code> will show the directories in your search path. Either copy the samtools executable there or add its location to the $PATH variable. You would be well served with a unix command line course or tutorial.</p>
  