Database Installation

The funannotate2 install command is used to download and install the databases required for gene prediction and functional annotation.

Basic Usage

To install all databases:

funannotate2 install -d all

Required Arguments

-d, --db: Databases to install [all,merops,uniprot,dbCAN,pfam,go,mibig,interpro,gene2product,mito]

Optional Arguments

-s, --show: Show currently installed databases (default: False)
-w, --wget: Use wget for downloading (default: False)
-f, --force: Force re-download/re-install of all databases (default: False)
-u, --update: Update databases if change detected (default: False)

Available Databases

The following databases can be installed:

all: Install all databases
merops: MEROPS protease database
uniprot: UniProtKB/Swiss-Prot database
dbCAN: Database for Carbohydrate-active enzyme ANnotation
pfam: Pfam protein families database
go: Gene Ontology database
mibig: Minimum Information about a Biosynthetic Gene cluster
interpro: InterPro protein families database
gene2product: Curated gene names and product descriptions
mito: Mitochondrial genome database

Showing Installed Databases

To see which databases are currently installed:

funannotate2 install -s

This will display a list of installed databases, their versions, and installation dates.

Updating Databases

To update all installed databases:

funannotate2 install -d all -u

This will check each database for updates and download new versions if available.

Forcing Reinstallation

To force reinstallation of a database:

funannotate2 install -d pfam -f

This will delete the existing database and download it again, regardless of whether it’s already installed.

Database Location

Databases are installed in the directory specified by the $FUNANNOTATE2_DB environment variable. This variable must be set before running the install command.

To set the environment variable:

# For bash/zsh
export FUNANNOTATE2_DB=/path/to/database/directory

# For csh/tcsh
setenv FUNANNOTATE2_DB /path/to/database/directory

You can add this line to your shell’s startup file (e.g., ~/.bashrc, ~/.zshrc) to make it permanent.

Database Information

Information about installed databases is stored in the funannotate-db-info.json file in the database directory. This file contains:

Database names
Installation dates
Version information
File paths

This information is used by other funannotate2 commands to locate the required databases.

Troubleshooting

If you encounter issues with database installation:

Check disk space: Ensure you have enough disk space for the databases (several GB may be required)
Check permissions: Ensure you have write permissions to the database directory
Check internet connection: Ensure you have a stable internet connection
Try wget: Use the -w option to use wget instead of the default downloader
Check logs: Look for error messages in the output

If problems persist, try installing databases individually rather than all at once.