text: user16328: I'm trying to run the python library called how_are_we_stranded_here. I have installed with pip install how_are_we_stranded_here. I have also installed its dependencies i.e kallisto 0.44.0 and RSeQC. On how_are_we_stranded_here's pypi page, it gives the following command under the usage heading:
   check_strandedness --gtf Yeast.gtf --transcripts Yeast_cdna.fasta \
  --reads_1 Sample_A_1.fq.gz --reads_2 Sample_A_2.fq.gz
  
  So I tried running the program in the terminal using my own files, the command was:
      check_strandedness --gtf Glycine_max.Glycine_max_v2.1.55.gtf \
  --transcripts Glycine_max.Glycine_max_v2.1.cdna.all.fa \
  --reads_1 SRR2079644.fastq
  
  But it keeps giving the error
  
  ./how_stranded.sh: line 1: check_strandedness: command not found
  
  I will be very thankful for any help on how to run it.
  
  user3848: pip should just work, anyway... Two approaches, point 1 is a last resort approach (not recommended), I definitely recommend point 2.
  First try,
  python3 -m pip install --upgrade how_are_we_stranded_here
  
  Try again does it work? Error logs?, then possibly ...
  
  You need to find out where it is,
  
     pip show how_are_we_stranded_here
     pip show check_strandedness
     pip show how_stranded.sh
  
  What you really want is the check_strandedness
  cd ~
  mkdir bin
  ./pathtoapp/check_stranded # make sure it works
  ln -si /pathwaytoapp/how_stranded.sh /home/whatever/bin/
  ln -si /pathwaytoapp/check_strandedness ~/bin/check_strandedness
  
  Then write
  export PATH="/home/whatever/bin:$PATH"
  
  or modify .profile or .bashrc, then
  source ~/.bash_profile
  
  Try again ...
  
  It is better to perform a conda installation
  
  Install either,
  
  Miniconda or;
  Anaconda
  
      conda install -c bioconda how_are_we_stranded_here
      conda create --name stranded
      conda activate stranded
      check_strandedness -h
  
  
original_text: 16328: <p>I'm trying to run the python library called how_are_we_stranded_here. I have installed with <code>pip install how_are_we_stranded_here</code>. I have also installed its dependencies i.e kallisto 0.44.0 and RSeQC. On how_are_we_stranded_here's pypi page, it gives the following command under the usage heading:</p>
  <pre><code> check_strandedness --gtf Yeast.gtf --transcripts Yeast_cdna.fasta \
  --reads_1 Sample_A_1.fq.gz --reads_2 Sample_A_2.fq.gz
  </code></pre>
  <p>So I tried running the program in the terminal using my own files, the command was:</p>
  <pre><code>    check_strandedness --gtf Glycine_max.Glycine_max_v2.1.55.gtf \
  --transcripts Glycine_max.Glycine_max_v2.1.cdna.all.fa \
  --reads_1 SRR2079644.fastq
  </code></pre>
  <p>But it keeps giving the error</p>
  <blockquote>
  <p>./how_stranded.sh: line 1: check_strandedness: command not found</p>
  </blockquote>
  <p>I will be very thankful for any help on how to run it.</p>
   3848: <p><code>pip</code> should just work, anyway... Two approaches, point 1 is a last resort approach (not recommended), I definitely recommend point 2.</p>
  <p>First try,</p>
  <pre><code>python3 -m pip install --upgrade how_are_we_stranded_here
  </code></pre>
  <p>Try again does it work? Error logs?, then possibly ...</p>
  <ol>
  <li>You need to find out where it is,</li>
  </ol>
  <pre><code>   pip show how_are_we_stranded_here
     pip show check_strandedness
     pip show how_stranded.sh
  </code></pre>
  <p>What you really want is the <code>check_strandedness</code></p>
  <pre><code>cd ~
  mkdir bin
  ./pathtoapp/check_stranded # make sure it works
  ln -si /pathwaytoapp/how_stranded.sh /home/whatever/bin/
  ln -si /pathwaytoapp/check_strandedness ~/bin/check_strandedness
  </code></pre>
  <p>Then write</p>
  <pre><code>export PATH=&quot;/home/whatever/bin:$PATH&quot;
  </code></pre>
  <p>or modify <code>.profile</code> or <code>.bashrc</code>, then</p>
  <pre><code>source ~/.bash_profile
  </code></pre>
  <p>Try again ...</p>
  <ol start="2">
  <li>It is better to perform a conda installation</li>
  </ol>
  <p>Install either,</p>
  <ul>
  <li><a href="https://docs.conda.io/en/latest/miniconda.html" rel="nofollow noreferrer">Miniconda</a> or;</li>
  <li><a href="https://docs.anaconda.com/anaconda/install/index.html" rel="nofollow noreferrer">Anaconda</a></li>
  </ul>
  <pre><code>    conda install -c bioconda how_are_we_stranded_here
      conda create --name stranded
      conda activate stranded
      check_strandedness -h
  </code></pre>
  