eggNOG-mapper Installation

eggNOG-mapper is a tool for fast functional annotation of novel sequences using precomputed orthologous groups and functional information.

Requirements

### Software Requirements

  • Python 3.7 or greater

  • BioPython >=1.76 (1.78 should also work for emapper v2.1.7)

  • psutil >=5.7.0

  • xlsxwriter >=1.4.3 (only if using the –excel option)

  • wget (Linux command; required for downloading databases with download_eggnog_data.py or creating new Diamond/MMseqs2 databases)

  • sqlite >=3.8.2

### Storage Requirements

  • ~40 GB for the eggNOG annotation databases (eggnog.db and eggnog.taxa.db)

  • ~9 GB for Diamond database (required if using -m diamond)

  • ~11 GB for MMseqs2 database (~86 GB if full MMseqs2 index is created; required if using -m mmseqs)

  • ~3 GB for PFAM database (required if using –pfam_realign options)

Database sizes depend on the selected taxonomic range. See: - HMMER databases: http://eggnog5.embl.de/#/app/downloads - Diamond/MMseqs2 databases: size depends on number of proteins in the taxonomic range

### Memory Requirements

  • Using –dbmem loads the entire eggnog.db into memory (~44 GB required)

  • Using –num_servers when running HMMER in server mode may increase memory usage proportionally

Installation

### PyPI Version

pip install eggnog-mapper

To install a specific version:

pip install 'eggnog-mapper==<version>'

### Conda (Bioconda Channel)

conda install -c bioconda -c conda-forge eggnog-mapper

### GitHub Release

  1. Download the latest version: https://github.com/eggnogdb/eggnog-mapper/releases/latest

  2. Decompress the .tar.gz or .zip file

  3. Enter the decompressed directory and install dependencies:

# Using setuptools
python setup.py install

# Using pip
pip install -r requirements.txt

# Using conda
conda install --file requirements.txt

### Cloning from GitHub

git clone https://github.com/eggnogdb/eggnog-mapper.git
cd eggnog-mapper
# Then install dependencies as above

Setup

Add eggNOG-mapper scripts and binaries to your PATH for convenience:

export PATH=/home/user/eggnog-mapper:/home/user/eggnog-mapper/eggnogmapper/bin:"$PATH"

Optionally, define a directory for the eggNOG-mapper databases:

export EGGNOG_DATA_DIR=/home/user/eggnog-mapper-data

Download the databases:

download_eggnog_data.py

  • By default, files are downloaded to data/ within the eggNOG-mapper directory if no EGGNOG_DATA_DIR or –data_dir is specified.

  • The Diamond database is optional; you can also use HMMER or MMseqs2.

  • For taxonomic-specific Diamond/MMseqs2 databases, use:

create_dbs.py -m diamond --dbname bacteria --taxa Bacteria

Optional Tools

eggNOG-mapper can use bundled binaries for the following tools:

  • Prodigal: required for –itype genome or –itype metagenome with –genepred prodigal

  • Diamond: required for -m diamond searches

  • MMseqs2: required for -m mmseqs searches

  • HMMER: required for -m hmmer and PFAM realignment options

If the tools are already installed on your system, eggNOG-mapper will use the versions found in your PATH. Otherwise, it uses the bundled binaries.