sphong/humann repository overview

⁠docker-humann

Docker image for HUMAnN

⁠Introduction

• HUMAnN is a great tool for functional analysis of whole metagenome sequencing data.
• This docker image may facilitate the usage of the software.
• Visit the following link for information on the program.
  • https://huttenhower.sph.harvard.edu/humann⁠
  • https://github.com/biobakery/humann⁠
• HUMAnN versions: 3.7 (tag: 3.7; latest)

⁠Links

• GitHub Link: https://github.com/sp1020/docker-humann⁠
• DockerHub Link: https://hub.docker.com/repository/docker/sphong/humann⁠

⁠Quick Start

⁠HUMAnN Database Setup

(*) Download database only on the first occasion. (The procedure may take about an hour.)

• Download database on local machine.
  • Place the databases out of the image.
  • Mount the databases when creating containers.

Step 1. Replace the database directory name

• Open the download_databases.sh script
• Specify dir_db as the directory where the database will be downloaded.

dir_db="/data/database/HUMAnN/201901b"

Step 2. Download database

• Execute the download_database.sh script.

./download_databases.sh 

Step 3. Download MetaPhlAn database

• Edit the download_mpa_db.sh file: dir_db
  • Specify dir_db as the directory where the MetaPhlAn database will be downloaded.
    • ⚠ Example: /data/database/MetaPhlAn/vOct22
  • (Optional) Specify db_index for the database
    • ⚠ For HUMAnN 3.7 use vOct22 version (mpa_vOct22_CHOCOPhlAnSGB_202212); more recent version conflict with other HUMAnN databases.
    • Do not modify the database unless there is a specific reason to do so.
• Execute the download script

./download_mpa_db.sh

• Consult the MetaPhlAn Docker image documentation below for details on the MetaPhlAn Docker image.
  • https://github.com/sp1020/docker-metaphlan⁠

⁠Execute HUMAnN commands

• Execute HUMAnN.
  • ⚠ Mount HUMAnN database to /database directory
  • ⚠ Mount MetaPhlAn database to /database_mpa
  • ⚠ Set --metaphlan-options with metaphlan_index
    • --metaphlan-options "--bowtie2db /database_mpa --index <MetaPhlAn-index>"

Example Codes

docker run --rm -v $PWD:/data \
    -v $db_humann:/database \
    -v $db_metaphlan:/database_mpa \
    -e USER_ID=$(id -u) \
    -e GROUP_ID=$(id -g) \
    sphong/humann \
    humann \
    --input inputs/demo.fastq.gz \
    --output results/demo_fastq \
    --metaphlan-options "--bowtie2db /database_mpa --index $metaphlan_index" \
    --threads 20

Refer to the scripts located in the examples directory

⁠Prerequisite

• docker
• docker image: sphong/metaphlan
  • Required to download MetaPhlAn database.

⁠License

• MIT License

⁠Maintainers

• Seungpyo Hong at Jeonbuk National University

⁠Acknowledgements

• HUMAnN