skills.rest
cpanse
cpanseCOMMUNITY
Explore all skills by this author →
WebsiteGitHub

fgcz-modules

Manage Lmod environment modules and install bioinformatics software on FGCZ Debian 12 servers.

Updated May 28, 2026
Search Tags:#bioinformatics#conda#pixi#software installation#fgcz#lmod#module load
One-click install
npx skills add https://github.com/cpanse/skills --skill fgcz-modules-cpanse
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: fgcz-modules
Source: https://github.com/cpanse/skills/tree/main/fgcz-infrastructure/skills/fgcz-modules
Command: npx skills add https://github.com/cpanse/skills --skill fgcz-modules-cpanse

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve? Bioinformatics work at FGCZ requires loading the correct software versions (R, Python, CellRanger, samtools) and installing new tools as system modules, which involves Lmod commands, Lua module files, NFS-shared paths, and server-specific rules that are easy to get wrong. ## Core Features & Use Cases - Module Management: Load, search, list, and troubleshoot Lmod modules across categories like Dev, Aligner, QC, Tools, and Variants, including common combinations for single-cell, spatial, and Python workflows. - Software Installation: Step-by-step procedures for compiling software, writing Lua module files, and committing them to the version-controlled module repository on fgcz-r-029. - Pixi & Conda Environments: Configure pixi with shared cache paths, SBATCH integration, and GPU-node setup, plus guidance on production vs development conda environments. - Use Case: You need CellRanger 10.0.0 for a new single-cell project. Use this Skill to load the right module combination, or to install a brand-new tool version as a proper system module with a git-committed Lua file. ## Quick Start Ask the agent to load the modules needed for single-cell RNA-seq analysis with R and CellRanger on the FGCZ servers.

Frequently Asked Questions about fgcz-modules

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

FAQPage Schema
How do I load CellRanger or R modules on FGCZ servers?▼

Use module load with the category path, for example module load Dev/R/4.5.0 and module load Aligner/CellRanger/10.0.0. Search available versions first with module spider CellRanger or module avail.

How do I install a new software module at FGCZ?▼

Installations must run on fgcz-r-029 via SSH. Compile the software into $ngpkg/Category/Name/Version, create a Lua module file in $ngmdf, test with module load, then commit the Lua file to the git repository in /usr/local/ngseq/etc.

What is the difference between production and dev Python modules?▼

Production modules like Dev/Python/3.12.8 are read-only conda environments, while the _dev variants allow installing packages with pip. Never modify production environments with the gi_ prefix.

Why should I avoid LD_LIBRARY_PATH when writing module files?▼

LD_LIBRARY_PATH causes runtime issues and conflicts across modules. Use LD_RUN_PATH or LIBRARY_PATH in Lua module files instead to set library search paths safely.

How do I use pixi on FGCZ without filling my home quota?▼

Loading Dev/pixi sets PIXI_CACHE_DIR and PIXI_HOME to shared /misc/fgcz01 paths. Delete the local .pixi directory after analysis, commit pixi.toml and pixi.lock to git, and add .pixi/ to .gitignore.

Related Skills

Explore More Software Engineering Skills→
caseywdunncaseywdunn
2

dunnlab-bioinformatics

Standardize Dunn Lab bioinformatics project scaffolding and data hygiene workflows.

Community
Advanced
pwwangpwwang
22

modulescorecalculator

Calculate per-cell module scores for Seurat single-cell data.

Community
Advanced
CodingKaiserCodingKaiser
6

bfabricpy

Provide a Python client for B-Fabric LIMS CRUD operations and relational reads.

Community
Intermediate
ClawBioClawBio
1.1k

repro-enforcer

Export bioinformatics analyses as reproducible bundles with Conda, containers, and pipelines.

Official
Intermediate