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Softwares

Benchmarking requires all dependent softwares to be installed beforehand.

1. Install most softwares via conda

For most softwares, a conda yaml file cellsnp-lite.benchmark.conda.yml is provided, which is aimed to make the installation easier by simply running,

conda env create -f cellsnp-lite.benchmark.conda.yml

Then the softwares would be installed to a new conda env named CSP. The global variable BIN_DIR in config.sh should be set to absolute path to the bin dir of CSP env (something like ~/.anaconda3/envs/CSP/bin).

2. Install remaining softwares manually

Vartrix

Besides, vartrix should be downloaded with

wget https://github.com/10XGenomics/vartrix/releases/download/v1.1.16/vartrix_linux

and then unzipped and copied to BIN_DIR.

R packages

Lastly, there are several R packages needed to be installed manually in CSP env: argparse, tibble, stringr, ggplot2, dplyr, tidyr, ggrepel by

conda activate CSP
R
# then install.packages(<package>) in R