CU Anschutz-HPC-documentation

All documentation associated with bioinformatics tutorial on the Alpine cluster.

Overview:

With this repository, HPC Anschutz users will fine shorts and concise documentation on bioinformatics Alpine related topics. This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

This repository is composed of two blocks: (1) An FAQ block, (2) An Alpine pipeline optimization FAQ and (3) A Quickbytes tutorial block.

I- FAQ:

• For questions regarding Alpine maintenance and globus related information please visit here.

II- Alpine pipeline optimization FAQ:

• For questions regarding Alpine pipeline optimization please visit here.

III- Quickbytes:

Quickbytes that are designed for package installation and pipeline optimization.

• R packages installation:

  • AldeX2 package installation
  • EcholocatoR package installation
  • CellRangerRkit related packages including devtools
  • Rstudio env/path setup for package installation
  • Reuse your Rstudio ENV with slurm
  • The little guide to address what R infrastructure I should use on Alpine

• Slurm related operations:

  • How to make slurm job arrays on Alpine?

• MATLAB installation in Juputerlab:

  • MATLAB-kernel-installation

• Github ssh:

  • If you want to set up your Github ssh on keys Alpine please follow this guide from CU Boulder.

• Deep learning applications installation on Alpine:

  • Pytorch-CUDA
  • Tensorflow-CUDA
  • DeepLabCut-CUDA
  • Dorado with Cuda
  • CellBender with Cuda

• Guide to use miniforge instead of anaconda on Alpine:

  • Miniforge guide on Alpine

• AMD gpu diversification on Alpine:

  • Adapt an NVIDIA pytorch pipeline to AMD

• Spark+Hail:

  • Spark+Hail interactive guide
  • Spark+Hail batch script guide

• Data transfers:

  • Globus transfer guide on Alpine with FAQ
  • Cyberduck transfer guide
  • For marginal cases only, please consider our Data transfer hub guide to transfer data from a CU Anschutz server to Alpine.

IV- Office hours presentation slides:

• Gnu parallel

V- Alpine storage:

• Petalibrary

VI- Lab workshops:

Workshops given to customized to labs that have been already given. Send an email to rc-help@colorado.edu to request a workshop.

• List of workshops:
  • NVIDIA Mark III Sys workshop series (05/04/23 to 06/22/23). Additional information can be found here.
  • Introduction to the Shell - Barocas lab
  • Introduction to Slurm - Barocas lab
  • Introduction to Alpine - Kalpathy-Cramer lab
  • Introduction to Slurm and Petalibrary - Lange lab
  • GPU partitions on Alpine Janani lab 09/06/23
  • Alpine entry level workshop 09/07/23
  • Immuno 6110 class 09/07/23
  • Intro to spack part 1 10/17/23
  • Intro to Horovod part 1 10/24/23
  • Alpine entry level workshop 11/02/23
  • Intro to GPU computing part 1 11/28/23
  • Intro to GPU computing part 2 11/30/23
  • Intro to GPU computing part 3 12/04/23
  • Alpine for noobs workshop 12/07/23
  • AMD_GPU_computing_022924
  • Alpine_entry_level_workshop_03/05/24
  • NVIDIA Mark III Sys workshop series Spring 2024 (01/25/24 to 05/02/24)
  • Alpine workshop to Uhler's lab (11/25/24)
  • GPUs on Alpine Pividori lab (01/15/25)
  • Alpine Best Practices Workshop
  • Containers on Alpine Workshop (04/01/25)
  • Alpine workshop on gpu partitions BARL JC (04/10/25)
  • Globus and rclone workshop (09/08/25)
  • Introduction to Alpine workshop (09/09/25)
  • Alpine module stack and miniforge (09/15/25)
  • Workshop: How to use R on Alpine? (09/22/25)