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Software

For more information about how to use the software, click the software name(link) below.

Job scheduler

Job scheduler automatically allocates computer resources (CPU core and memory) to each user in an environment used by many users. It works as the Operating System when the entire cluster computer is viewed as one computer.

area namethe general analysis sectionthe personal genome section

Grid Engine

installedApplication Required

Slurm

Application Required

Package managers

The following package managers can be used only with user permission. They facilitate the construction of development and analysis environments.

area namethe general analysis sectionthe personal genome section

Guix

installed

Spack

availableavailable

Environmental Modules

installedinstalled

Container and analysis pipeline

area namethe general analysis sectionthe personal genome section

Singularity

installedinstalled
Rhelixa RNAseq pipelineinstalledApplication Required
DFASTavailableavailable

Bioinformatics Tools

Biocontainers Singularity Images

Singularity container images created by the BioContainers project (over 2,000 different analysis software and over 90,000 Singularity image files, including different versions) are available in /user/local/biotools directory.

For the contents and how to use the software, refer to Registry of the BioContainers' official website.

Data transfer and data sharing

area namethe general analysis sectionthe personal genome section

Aspera

available

HCPtools

Application Required

Development Environment and Libraries

Many development environments are preinstalled on the system. But if you need a specific version for purposes such as reproducing an analysis, you can either install them yourself because Many analysis environments can be installed with user permission or you can use the Singularity container.

area namethe general analysis sectionthe personal genome section

Python

availableavailable

R

availableavailable

Jupyter Notebook

availableavailable

Jupyter Lab

availableavailable

R Studio Server

availableavailable

Java

availableavailable

Node.JS, TypeScript

availableavailable

Rust

availableavailable

C/C++ (GCC)

installedinstalled

C/C++ (Intel Compiler)

installed

C/C++ (PGI Compiler)

installed

CUDA

installedinstalled
OpenMPavailableavailable
MPICHavailableavailable