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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.

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    $\begingroup$ You might need to include your pip install output too. The package defines a set of scripts that should get you check_strandedness in your path, and it works for me... so I bet something didn't work right during install. $\endgroup$
    – Jesse
    Dec 10, 2022 at 15:29
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    $\begingroup$ 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. $\endgroup$ Dec 13, 2022 at 22:03

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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 ...

  1. It is better to perform a conda installation

Install either,

    conda install -c bioconda how_are_we_stranded_here
    conda create --name stranded
    conda activate stranded
    check_strandedness -h
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    $\begingroup$ 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. $\endgroup$
    – pubsurfted
    Dec 11, 2022 at 17:30
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    $\begingroup$ No problem @pubsurfted, although this one is not 'solved' upvotes always welcome. $\endgroup$
    – M__
    Dec 11, 2022 at 19:12
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    $\begingroup$ upvoted. Thank you! $\endgroup$
    – pubsurfted
    Dec 12, 2022 at 4:14

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