High-Performance Computing at the NIH
Repositories for tools developed by the NIH HPC staff. These tools are made available here as a courtesy, without any guarantee of support
Bethesda, MD, USA
Pinned Repositories
gpu4singularity
Add GPU support to your Singularity container!
pbs2slurm
Translate PBS batch scripts to Slurm
python-in-hpc
Materials for a Python in HPC class
singularity-def-files
definition files and wrapper scripts used by NIH HPC staff to install user-facing apps on the Biowulf cluster
singularity-examples
example singularity definition files and demos
Singularity-Tutorial
How to use Singularity!
snakemake-class
Class materials for the NIH HPC snakemake class
snakemake_profile
Minimal snakemake profile for biowulf cluster
spark-slurm
Tool for running/managing ad hoc spark clusters on a Slurm cluster
swarm
Swarm is a script designed to simplify submitting a group of commands to the Biowulf cluster.
High-Performance Computing at the NIH's Repositories
NIH-HPC/Singularity-Tutorial
How to use Singularity!
NIH-HPC/python-in-hpc
Materials for a Python in HPC class
NIH-HPC/singularity-def-files
definition files and wrapper scripts used by NIH HPC staff to install user-facing apps on the Biowulf cluster
NIH-HPC/singularity-examples
example singularity definition files and demos
NIH-HPC/spark-slurm
Tool for running/managing ad hoc spark clusters on a Slurm cluster
NIH-HPC/snakemake-class
Class materials for the NIH HPC snakemake class
NIH-HPC/gpu4singularity
Add GPU support to your Singularity container!
NIH-HPC/pbs2slurm
Translate PBS batch scripts to Slurm
NIH-HPC/swarm
Swarm is a script designed to simplify submitting a group of commands to the Biowulf cluster.
NIH-HPC/snakemake_profile
Minimal snakemake profile for biowulf cluster
NIH-HPC/idep
Integrated Differential Expression and Pathway analysis
NIH-HPC/julia-for-scientific-computing
Materials for introductory Julia class
NIH-HPC/toil
A scalable, efficient, cross-platform and easy-to-use workflow engine in pure Python
NIH-HPC/biowulf_ray
Sample submit script for running ray on biowulf
NIH-HPC/hotnet2
HotNet2 is an algorithm for finding significantly altered subnetworks in a large gene interaction network
NIH-HPC/portauthority
find a free TCP port
NIH-HPC/singularityware.github.io
base documentation site for Singularity software
NIH-HPC/tensorflow
moved to https://github.com/NIH-HPC/singularity-examples
NIH-HPC/GEMSCAN
Joint variant calling with GATK4 HaplotypeCaller, Google DeepVariant 1.0.0 and Strelka2, coordinated via Snakemake.
NIH-HPC/keras_demo
moved to https://github.com/NIH-HPC/singularity-examples/tree/master/keras
NIH-HPC/pyslurm
Python Interface to Slurm
NIH-HPC/relion
Image-processing software for cryo-electron microscopy
NIH-HPC/rslurm
Submit R code to a Slurm cluster
NIH-HPC/singularity
Singularity: Application containers for Linux
NIH-HPC/Winnowmap
Long read / genome alignment software
NIH-HPC/ximmer
Ximmer is a system for CNV calling on exome and targeted genomic sequencing