Installation of the kmer_tools conda evironment

These instructions assume you have already conda installed (e.g. miniconda, anaconda, mamba). To check your conda is function you can execute

conda --help

if you don't see the conda help page, do not proceed further.

Setting up conda

Set up a new conda envirnment and activate it

conda create -n kmer_tools
conda activate kmer_tools

note that you can save condas to alternative places by specifying something like --prefix=/full/path/to/conda/env/kmer_tools instead of the parameter -n.

Now we can proceed by installing individual k-mer tools. Once you will execute following lines, it will be fetching the data from the repositories for a moment and prompt you to confirm you want to download the 400MB of packages (contains both python and R, therefore the relatively big size)

conda install -c bioconda numpy smudgeplot kmc kat

And finally, install Genomescope 2.0 (that is unfortunately not on conda). First, download it, then enter the directory and start an R session

git clone https://github.com/tbenavi1/genomescope2.0
cd genomescope2.0
R

now, within R run following commnads to install 2 dependencies and the genomescope package

install.packages('minpack.lm', repos = "http://cran.us.r-project.org")
install.packages('argparse', repos = "http://cran.us.r-project.org")
install.packages('.', repos=NULL, type="source")
q() # quit R

and the one last step is to copy the genomescope execution script to your conda (again in your shell)