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 name	the general analysis division	the personal genome analysis division
Grid Engine	installed	Application 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 name	the general analysis division	the personal genome analysis division
Environmental Modules	X	X (Only available for CentOS 7)
Spack	available	available

Container

area name	the general analysis division	the personal genome analysis division
Apptainer (Singularity)	installed	installed
BioContainers Apptainer (Singularity) Images	installed	installed

Analysis pipeline

area name	the general analysis division	the personal genome analysis division
DFAST	available	available
NBDC-DDBJ Imputation Server	available(※Demo function in preparation)	Application Required
NVIDIA Parabricks	☓	Application Required
Rhelixa RNAseq pipeline	installed	available

Data transfer and data sharing

area name	the general analysis division	the 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 name	the general analysis division	the personal genome analysis division
Python	available	available
R	available	available
Jupyter Notebook	available	available
Jupyter Lab	available	available
R Studio Server	available	available
Java	available	available
Node.JS, TypeScript	available	available
Rust	available	available
C/C++ (GCC)	installed	installed
C/C++ (Intel Compiler)	installed	☓
C/C++ (PGI Compiler)	installed	☓
CUDA	installed	installed
OpenMP	available	available
MPICH	available	available