Databases

Install Databases

Attention

Before executing the full workflow, install all required databases by running

snakemake --profile profile/ databases/.setup_done

In general

Databases are downloaded automatically (annoSnake always uses the latest available database versions if possible). However, you can use your own protein databases, which must be saved in the correct format (see below). Check out ./rules/setup_databases.smk for how annoSnake sets up databases. The file .setup_done in each database subdirectory is necessary to run the workflow correctly. So if you want to use your own databases, make sure that there is one in the respective subdirectories (touch .setup_done). If you need any help, please visit GitHub and open a New issue.

workflow/databases/
├── cazymes/
|       ├── dbCAN-fam-HMMs.txt.v11
│       ├── dbCAN-fam-HMMs.txt.v11.h3f
│       ├── dbCAN-fam-HMMs.txt.v11.h3i
│       ├── dbCAN-fam-HMMs.txt.v11.h3m
│       ├── dbCAN-fam-HMMs.txt.v11.h3p
│       └── .setup_done
├── checkm/
|       ├── distributions/
│       ├── ...
│       └── .setup_done
├── fetchMGs/
|       ├── bin/
|       ├── ...
|       └── .setup_done
├── gtdb/
|       ├── gtdb_vers202_metadata.csv
│       ├── gtdb_vers202/
|       ├── ...
│       └── .setup_done
├── gtdb_tk/
|       └── .setup_done
├── kegg/
│       ├── ko_list
│       ├── profiles/
│       └── .setup_done
├── microbeannotator/
|       ├── conversion.db
|       ├── ...
|       └── .setup_done
├── pfam/
|       ├── Pfam-A.hmm
|       ├── ...
|       └── .setup_done
└── quast/
      ├── metaquast.py
      ├── ...
      └── .setup_done