Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-12-11T17:30:21.130Z
Answers.Text: Thank you so much for taking out the time to give such a thorough reply. It definitely solved the check-strandedness issue but opened a plethora of other issues, so I just gave up.
Answers.UserDisplayName: pubsurfted
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-12-11T19:12:13.170Z
Answers.Text: No problem @pubsurfted, although this one is not 'solved' upvotes always welcome.
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-12-12T04:14:34.773Z
Answers.Text: upvoted. Thank you!
Answers.UserDisplayName: pubsurfted
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-12-10T15:32:19.067Z
Answers.LastActivityDate: 2022-12-10T15:45:32.150Z
Answers.LastEditDate: 2022-12-10T15:45:32.150Z
Answers.UserDisplayName: M__
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-12-10T15:29:50.067Z
Comments.Text: You might need to include your pip install output too.  The package [defines a set of scripts](https://github.com/signalbash/how_are_we_stranded_here/blob/f964c9bc94c99cd119a99029aeb5a73d487f14e0/setup.py#L48) that should get you `check_strandedness` in your path, and it works for me... so I bet something didn't work right during install.
Comments.UserDisplayName: Jesse
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-12-13T22:03:47.577Z
Comments.Text: Would you consider installing this in a conda environment or other virtual environment, to control the background more effectively (with regard to M__'s answer and your comment below). It sounds like there are some issues in the background that might need resolving.
Comments.UserDisplayName: Maximilian Press
Tags: <rna-seq>
Title: How to run how_are_we_stranded_here?
ThreadText: # How to run how_are_we_stranded_here?
  
  (Asked by: username_0 on 2022-12-10)
  
  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.
  
  **Tags:** rna-seq
  
  > **Comments:**
  > **username_1**: You might need to include your pip install output too.  The package [defines a set of scripts](https://github.com/signalbash/how_are_we_stranded_here/blob/f964c9bc94c99cd119a99029aeb5a73d487f14e0/setup.py#L48) that should get you `check_strandedness` in your path, and it works for me... so I bet something didn't work right during install.  
  > **username_2**: Would you consider installing this in a conda environment or other virtual environment, to control the background more effectively (with regard to M__'s answer and your comment below). It sounds like there are some issues in the background that might need resolving.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2022-12-10. Score: 2 | Accepted answer
  
  `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 ...
  
  1. 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 ...
  
  2. It is better to perform a conda installation
  
  Install either,
  
  * [Miniconda](https://docs.conda.io/en/latest/miniconda.html) or;
  * [Anaconda](https://docs.anaconda.com/anaconda/install/index.html)
  
  ```
      conda install -c bioconda how_are_we_stranded_here
      conda create --name stranded
      conda activate stranded
      check_strandedness -h
  
  ```
  
  > **Comments:**
  > **username_0**: Thank you so much for taking out the time to give such a thorough reply. It definitely solved the check-strandedness issue but opened a plethora of other issues, so I just gave up.  
  > **username_3**: No problem @username_0, although this one is not 'solved' upvotes always welcome.  
  > **username_0**: upvoted. Thank you!  
  
  ---
  
  