<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>

CC BY-SA 4.0
2022-12-11T17:30:21.130Z
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.
pubsurfted
CC BY-SA 4.0
2022-12-11T19:12:13.170Z
No problem @pubsurfted, although this one is not 'solved' upvotes always welcome.
M__
CC BY-SA 4.0
2022-12-12T04:14:34.773Z
upvoted. Thank you!
pubsurfted
CC BY-SA 4.0
2022-12-10T15:32:19.067Z
2022-12-10T15:45:32.150Z
2022-12-10T15:45:32.150Z
M__
<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>

CC BY-SA 4.0
2022-12-10T15:29:50.067Z
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.
Jesse
CC BY-SA 4.0
2022-12-13T22:03:47.577Z
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.
Maximilian Press
<rna-seq>
How to run how_are_we_stranded_here?
# 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 ...

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

> **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 @pubsurfted, although this one is not 'solved' upvotes always welcome.  
> **username_0**: upvoted. Thank you!  

---

