setup

name	setup
description	First-time environment and database setup for shotgun metagenomics tool skills. Use this skill when: (1) Installing Conda/Micromamba environments, (2) Preparing host, taxonomy, function, GTDB, or CheckM2 databases, (3) Installing BASALT weights, (4) Onboarding a new compute node. For public database routing (SRA/ENA, MGnify, GTDB releases, bioBakery), use public-databases and the matching resource skill. For individual tools, use the matching software skill (fastp, kneaddata, ...).
license	MIT
category	utilities
tags	["setup","onboarding","installation","conda"]

Setup

Analytical thinking

Install software and databases once, version-pin them, and keep analysis runs reproducible. Prefer one env per major tool family when dependency conflicts arise.

Public resources are a separate layer — see public-databases before inventing ad-hoc download scripts.

Checklist

Step	Check	Next skill
Package manager	micromamba -V	—
Project dirs	seq/ temp/ result/	study-design
Public DB plan	Which archives/catalogues/indexes	public-databases
QC tools	fastp	fastp
Host depletion	KneadData + Bowtie2 host index	kneaddata
Profiling DBs	MetaPhlAn/HUMAnN/Kraken	biobakery-databases / kraken2
Assemblers	MEGAHIT / SPAdes	megahit / metaspades
Binning QC	CheckM2 DB	checkm2
Taxonomy runtime	GTDBTK_DATA_PATH	gtdb + gtdbtk
Binning tools	BASALT★ / MetaWRAP / DAS Tool	basalt (recommended) / metawrap / dastool
Function DBs	eggNOG / CARD	eggnog-mapper / rgi
BASALT weights	BASALT --help + $BASALT_WEIGHT (5 CSVs)	basalt

BASALT install (Conda edition)

See basalt skill and https://basalt-guide.readthedocs.io/en/latest/installation.html

git clone --branch V1.2.2 --depth 1 https://github.com/PKU-EMBL/BASALT.git
cd BASALT
micromamba create -n basalt -f basalt_environment.yml --strict-channel-priority --yes
micromamba run -n basalt bash install.sh

Related skills

public-databases · tool-selection · nextflow · snakemake · research-analysis · every software skill under skills/