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    28 repositories

    • swarm

      Public
      Swarm is a script designed to simplify submitting a group of commands to the Biowulf cluster.
      Perl
      •
      Other
      •7•8•0•0•Updated Jun 30, 2025Jun 30, 2025

    • af3

      Public
      Biowulf alphhafold3 wrapper
      Python
      •
      Other
      •1•0•0•0•Updated Mar 11, 2025Mar 11, 2025

    • snakemake_profile

      Public
      Minimal snakemake profile for biowulf cluster
      Python
      •2•10•0•0•Updated Jan 21, 2025Jan 21, 2025

    • slurm_log_tool

      Public
      Tool for colorizing slurm logs and counting events in slurm log
      Lex
      •0•0•0•0•Updated Dec 19, 2024Dec 19, 2024

    • Winnowmap

      Public
      Long read / genome alignment software
      C
      •
      Other
      •29•0•0•0•Updated Oct 24, 2024Oct 24, 2024

    • snakemake-class

      Public
      Class materials for the NIH HPC snakemake class
      Python
      •
      Other
      •10•15•0•0•Updated Sep 27, 2024Sep 27, 2024

    • pbs2slurm

      Public
      Translate PBS batch scripts to Slurm
      Python
      •
      Other
      •4•11•0•0•Updated Sep 11, 2024Sep 11, 2024

    • pyslurm

      Public
      Python Interface to Slurm
      Cython
      •
      GNU General Public License v2.0
      •124•0•0•0•Updated Feb 9, 2023Feb 9, 2023

    • rslurm

      Public
      Submit R code to a Slurm cluster
      R
      •32•0•0•0•Updated Oct 5, 2022Oct 5, 2022

    • GEMSCAN

      Public
      Joint variant calling with GATK4 HaplotypeCaller, Google DeepVariant 1.0.0 and Strelka2, coordinated via Snakemake.
      Python
      •
      MIT License
      •9•0•0•0•Updated Jul 6, 2022Jul 6, 2022

    • spark-slurm

      Public
      Tool for running/managing ad hoc spark clusters on a Slurm cluster
      Shell
      •11•25•0•0•Updated May 19, 2022May 19, 2022

    • biowulf_ray

      Public
      Sample submit script for running ray on biowulf
      Python
      •0•2•0•0•Updated Nov 9, 2021Nov 9, 2021

    • singularity-def-files

      Public
      definition files and wrapper scripts used by NIH HPC staff to install user-facing apps on the Biowulf cluster
      Shell
      •
      Other
      •5•32•1•0•Updated Mar 30, 2021Mar 30, 2021

    • julia-for-scientific-computing

      Public
      Materials for introductory Julia class
      Julia
      •
      Other
      •0•2•0•0•Updated Mar 27, 2021Mar 27, 2021

    • Singularity-Tutorial

      Public
      How to use Singularity!
      45•68•0•0•Updated Jun 3, 2020Jun 3, 2020

    • python-in-hpc

      Public
      Materials for a Python in HPC class
      Jupyter Notebook
      •
      Other
      •9•33•0•0•Updated Feb 20, 2020Feb 20, 2020

    • portauthority

      Public
      find a free TCP port
      Python
      •
      Other
      •0•1•0•0•Updated May 21, 2019May 21, 2019

    • idep

      Public
      Integrated Differential Expression and Pathway analysis
      R
      •63•2•0•0•Updated Mar 1, 2019Mar 1, 2019

    • singularity-examples

      Public
      example singularity definition files and demos
      singularity-containers
      Shell
      •12•27•0•0•Updated Jun 14, 2018Jun 14, 2018

    • singularityware.github.io

      Public
      base documentation site for Singularity software
      JavaScript
      •49•1•0•0•Updated May 7, 2018May 7, 2018

    • toil

      Public
      A scalable, efficient, cross-platform and easy-to-use workflow engine in pure Python
      Python
      •
      Apache License 2.0
      •244•2•0•0•Updated May 1, 2018May 1, 2018

    • ximmer

      Public
      Ximmer is a system for CNV calling on exome and targeted genomic sequencing
      JavaScript
      •
      GNU Lesser General Public License v2.1
      •11•0•0•0•Updated Feb 12, 2018Feb 12, 2018

    • tensorflow

      Public
      moved to https://github.com/NIH-HPC/singularity-examples
      0•1•0•0•Updated Nov 20, 2017Nov 20, 2017

    • keras_demo

      Public
      moved to https://github.com/NIH-HPC/singularity-examples/tree/master/keras
      4•0•0•0•Updated Nov 20, 2017Nov 20, 2017

    • singularity

      Public
      Singularity: Application containers for Linux
      C
      •
      Other
      •425•0•0•0•Updated Nov 15, 2017Nov 15, 2017

    • hotnet2

      Public
      HotNet2 is an algorithm for finding significantly altered subnetworks in a large gene interaction network
      Python
      •
      Other
      •43•1•0•0•Updated Oct 5, 2017Oct 5, 2017

    • gpu4singularity

      Public
      Add GPU support to your Singularity container!
      cudasingularitygpu-support
      Shell
      •
      Other
      •8•15•0•0•Updated Jul 20, 2017Jul 20, 2017

    • relion

      Public
      Image-processing software for cryo-electron microscopy
      C++
      •
      GNU General Public License v2.0
      •221•0•0•0•Updated May 9, 2017May 9, 2017