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@NIH-HPC

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

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  1. swarm swarm Public

    Swarm is a script designed to simplify submitting a group of commands to the Biowulf cluster.

    Perl 7 6

  2. python-in-hpc python-in-hpc Public

    Materials for a Python in HPC class

    Jupyter Notebook 33 9

  3. singularity-examples singularity-examples Public

    example singularity definition files and demos

    Shell 27 12

  4. snakemake-class snakemake-class Public

    Class materials for the NIH HPC snakemake class

    Python 16 10

  5. Singularity-Tutorial Singularity-Tutorial Public

    Forked from Singularity-tutorial/Singularity-tutorial.github.io

    How to use Singularity!

    66 20

  6. singularity-def-files singularity-def-files Public

    definition files and wrapper scripts used by NIH HPC staff to install user-facing apps on the Biowulf cluster

    Shell 29 5

Repositories

Showing 10 of 27 repositories
  • slurm_log_tool Public

    Tool for colorizing slurm logs and counting events in slurm log

    NIH-HPC/slurm_log_tool’s past year of commit activity
    Lex 0 0 0 0 Updated Dec 19, 2024
  • swarm Public

    Swarm is a script designed to simplify submitting a group of commands to the Biowulf cluster.

    NIH-HPC/swarm’s past year of commit activity
    Perl 7 6 0 0 Updated Nov 12, 2024
  • Winnowmap Public Forked from marbl/Winnowmap

    Long read / genome alignment software

    NIH-HPC/Winnowmap’s past year of commit activity
    C 0 24 0 0 Updated Oct 24, 2024
  • snakemake_profile Public

    Minimal snakemake profile for biowulf cluster

    NIH-HPC/snakemake_profile’s past year of commit activity
    Python 6 2 0 0 Updated Oct 4, 2024
  • snakemake-class Public

    Class materials for the NIH HPC snakemake class

    NIH-HPC/snakemake-class’s past year of commit activity
    Python 16 10 0 0 Updated Sep 27, 2024
  • pbs2slurm Public

    Translate PBS batch scripts to Slurm

    NIH-HPC/pbs2slurm’s past year of commit activity
    Python 11 4 0 0 Updated Sep 11, 2024
  • pyslurm Public Forked from PySlurm/pyslurm

    Python Interface to Slurm

    NIH-HPC/pyslurm’s past year of commit activity
    Cython 0 GPL-2.0 120 0 0 Updated Feb 9, 2023
  • rslurm Public Forked from earthlab/rslurm

    Submit R code to a Slurm cluster

    NIH-HPC/rslurm’s past year of commit activity
    R 0 32 0 0 Updated Oct 5, 2022
  • GEMSCAN Public Forked from NCI-CGR/GEMSCAN

    Joint variant calling with GATK4 HaplotypeCaller, Google DeepVariant 1.0.0 and Strelka2, coordinated via Snakemake.

    NIH-HPC/GEMSCAN’s past year of commit activity
    Python 0 MIT 8 0 0 Updated Jul 6, 2022
  • spark-slurm Public

    Tool for running/managing ad hoc spark clusters on a Slurm cluster

    NIH-HPC/spark-slurm’s past year of commit activity
    Shell 22 12 0 0 Updated May 19, 2022
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