HPC_installation_guide.md

In dyxmvp/seqExplorer: Single-cell data analysis

Installation guide on HPC

This is an installation guide of seqExplorer for HPC at Yale University, but it should also work for other HPC. This guide shows how to set up seqExplorer on Ruddle, Grace, and Farnam. The installation takes about 30 ~ 40 minutes.

1. Installation

Run the following commands:

srun --x11 --pty -p interactive -c 1 --mem=10g bash

module load R/3.5.0-foss-2016b-avx2

If you are using Grace cluster, add the following command:

module load Libs/HDF5/1.8.13-intel15

Then, run the following commands:

R

if (!require("devtools"))
  install.packages("devtools")

devtools::install_github('dyxmvp/seqExplorer')

Type "yes" and enter, if the system asks:

(1)

Would you like to use a personal library instead? (yes/No/cancel)

(2)

Would you like to create a personal library? (yes/No/cancel)

Select a CRAN mirror (for example: USA(CA 1)[https]), if the system asks:

--- Please select a CRAN mirror for the use in this session ---

After finished, exit R program using:

q()

2. Getting Started

Run the following commands:

srun --x11 --pty -p interactive -c 5 --mem=40g bash

module load R/3.5.0-foss-2016b-avx2

If you are using Grace cluster, add the following command:

module load Libs/HDF5/1.8.13-intel15

Then, run the following commands:

R

library(seqExplorer)

seqExplorer()

Finally, seqExplorer will launch with a browser.

3. Exit

To close seqExplorer, use ctrl+c to return to R or use ctrl+z to close all R program.

dyxmvp/seqExplorer documentation built on Aug. 22, 2020, 10:41 p.m.