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xihaoli / STAARpipeline

An R package for performing association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using STAARpipeline
GNU General Public License v3.0
58 stars 18 forks source link

preinstall packages #3

Closed JianqiaoWang closed 1 year ago

JianqiaoWang commented 1 year ago

I would suggest add following lines for the preinstall packages. These packages seem need to be installed manually in the order (like STAAR depend on SeqArray).

BiocManager::install("SeqArray") BiocManager::install("SeqVarTools") devtools::install_github("hanchenphd/GMMAT") BiocManager::install("GENESIS") devtools::install_github("xihaoli/STAAR",ref="main") BiocManager::install("TxDb.Hsapiens.UCSC.hg38.knownGene") BiocManager::install("GenomicFeatures") devtools::install_github("zilinli1988/SCANG")

I am also get confused for the Intel Math Kernel Library.

xihaoli commented 1 year ago

Hi Jianqiao,

Thank you for your suggestions. Alternatively, you could also pull the STAARpipeline docker image, which includes an R built with Intel MKL and all STAAR-related packages (STAAR, SCANG, STAARpipeline, STAARpipelineSummary) pre-installed.

Best, Xihao