Problems installing kb-python on R software (Windows 10)

Question

I am trying yo install to make an RNA-seq analysis from raw-data (fastq extension) and I am trying to install kb-python by running the next lines:

conda create -y --name kb python=3.8 #create an environment, specifying python v3.8
conda activate kb #activate that newly created environment
pip install kb-python #install kb-python in the environment.  Note: if this fails because of an issue with pysam, then do 'conda install pysam' then retry this line.

When I run the last line it takes many many hours (more than one day. I tried it with two PCs, one of 4GB and another one of 8GB of RAM and 300GB of storage).

Because of it takes so long the PC overheats and I have to turn off it to avoid physical damage. Any suggestion? Any alternative for performing an RNA-seq analysis.

I am following the next tutorial: https://protocols.hostmicrobe.org/conda

Many thanks!

Answer 1

It looks like kb-python is available through Anaconda (https://anaconda.org/bioconda/kb-python), so you could try installing with the command "conda install -c bioconda kb-python" instead. I came across the same time-intensive problem using pip. This conda install worked for me.

Your commands would look like so:

conda create -y --name kb python=3.8 #create an environment, specifying python v3.8
conda activate kb #activate that newly created environment
conda install -c bioconda kb-python #install kb-python in the environment.  Note: if this fails because of an issue with pysam, then do 'conda install pysam' then retry this line.