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installing-software

Install and configure software on the Yale SOM HPC cluster using modules, uv, and Apptainer.

5|1|Updated Apr 29, 2026
Search Tags:#uv#hpc#apptainer#module-system#software-installation#static-binaries#glibc-compatibility
One-click install
npx skills add https://github.com/yale-som-hpc/claude-code-marketplace --skill installing-software
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: installing-software
Source: https://github.com/yale-som-hpc/claude-code-marketplace/tree/main/plugins/hpc/skills/installing-software
Command: npx skills add https://github.com/yale-som-hpc/claude-code-marketplace --skill installing-software

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Installing software on the Yale SOM HPC cluster can be error-prone due to dependency conflicts, missing system permissions, and GLIBC compatibility issues. This Skill provides a guided approach to using cluster modules, uv/renv for language environments, and static/musl binaries, plus Apptainer containers, to simplify software setup without sudo.

Core Features & Use Cases

  • Module-first discovery and loading: Discover and load system software safely using Lmod modules.
  • Language environments with uv/renv: Manage Python and R environments per project without system-level changes.
  • Containerized stacks with Apptainer: Build or run reproducible environments when binaries have library conflicts.
  • Use Case: When you need to install a new tool on the cluster, do not modify system files; use modules or Apptainer.

Quick Start

Follow these steps to install a tool on the Yale SOM HPC cluster using modules, uv, and Apptainer.

Frequently Asked Questions about installing-software

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I install software on the Yale HPC cluster without sudo access?▼

Install software on the Yale HPC cluster without sudo by using Lmod modules for system tools, uv or renv for language environments, and Apptainer for containerized stacks.

What is the best way to resolve GLIBC compatibility issues when installing tools on an HPC cluster?▼

Resolve GLIBC compatibility issues on the cluster by deploying static or musl binaries, or by building and running Apptainer containers that bundle their own compatible libraries.

How do I manage Python and R environments per project on a shared file system?▼

Manage Python and R environments per project on shared file systems by using uv and renv to create isolated, reproducible language environments without modifying system-level dependencies.

When should I use Apptainer instead of loading cluster modules for software installation?▼

Use Apptainer instead of cluster modules when binary tools have library conflicts or require complex dependencies, ensuring reproducible containerized deployments across cluster jobs.

Does the module system work with containerized stacks for cluster jobs?▼

The module system works alongside containerized stacks by safely loading system software via Lmod, while Apptainer handles reproducible environments when binaries face library conflicts.

Why do my software installations fail with dependency conflicts on the cluster?▼

Software installations fail on the cluster due to dependency conflicts and GLIBC issues, which are avoided by using per-project local binaries, uv environments, and Apptainer containers.

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