| 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/
