iseq main package

Due to institutional restrictions, I cannot put source code in GitHub. Please email me directly if you want to download the iseq source code.

# Download the source code and gunzip
python setup.py install
# Or use pip
pip install .

iseq required softwares and databases

# Using BioInstaller
# install.packages("BioInstaller")
library(BioInstaller)
install.packages("optparse")
requirements = c("bwa", "samtools", "picard", "vcftools", "gatk",
                 "varscan2", "ANNOVAR", "tvc", "lofreq", "gatk_bundle")
dest.dir="~/opt/packages"
download.dir=paste0("~/opt/source_code/", requirements)
req.len <- length(requirements)
install.bioinfo(requirements, destdir = rep(dest.dir, req.len), download.dir = download.dir)