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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 divisionthe personal genome analysis division

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 divisionthe personal genome analysis division

Environmental Modules

XX (Only available for CentOS 7)

Spack

availableavailable

Container

area namethe general analysis divisionthe personal genome analysis division

Apptainer (Singularity)

installedinstalled

BioContainers Apptainer (Singularity) Images

installedinstalled

Analysis pipeline

area namethe general analysis divisionthe personal genome analysis division

DFAST

availableavailable

TogoImputation

available(※Demo function in preparation)Application Required

NVIDIA Parabricks

Application Required

Rhelixa RNAseq pipeline

installedavailable

Data transfer and data sharing

area namethe general analysis divisionthe personal genome analysis division

Archaea tools(formerly HCPtools)

available

Aspera

available

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 divisionthe personal genome analysis division

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

Go

availableavailable
OpenMPavailableavailable
MPICHavailableavailable