inst/htslib_version/README.md

In alexchwong/SpliceWiz: interactive analysis and visualization of alternative splicing in R

Enabling htslib mode

We recently implemented an htslib version of SpliceWiz's processBAM and BAM2COV functions, (namely processBAM_hts() and BAM2COV_hts()). To install an htslib-dependent version of SpliceWiz, you will need to clone the SpliceWiz repo and overwrite some files with htslib source files.

First, we recommend you install SpliceWiz as normal, if only to ensure you have the required R package dependencies.

From R:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.16")
BiocManager::valid()              # checks for out of date packages

BiocManager::install("SpliceWiz")

Then, from the command line, clone the repository and copy the contents of this directory to overwrite corresponding files from the root directory:

# Navigate to a directory of your choice, e.g.:
cd /path/to

git clone https://github.com/alexchwong/SpliceWiz
cd SpliceWiz
cp -r inst/htslib_version/* .

Then, from R:

# Roxygenize for documentation on processBAM_hts() and BAM2COV_hts()
devtools::document("/path/to/SpliceWiz")

# Install the package
install.packages(
    "/path/to/SpliceWiz", 
    repos = NULL, 
    type = "source"
)

alexchwong/SpliceWiz documentation built on March 17, 2024, 3:16 a.m.