1. Usage

Table of contents

• Intrduction
• How to install the pipeline
  • Local installation
  • Building containers
  • Download and build database
  • Cluster configuration
• Running the pipeline
• Updating the pipeline
• Usage

Introduction

LAGOON-MCL uses Nextflow as workflow manager, and Singlularity as container manager. If you're using it on a cluster, Nextflow handles job submission (SLURM, PBS, etc.).

How to install the pipeline?

Local installation

Check that Singularity and Nextflow are installed on your system.

git clone https://github.com/jroussea/lagoon-mcl.git
cd lagoon-mcl

Building containers

Containers of the tools used by LAGOON-MCL are available at BioContainers.

• Diamond (v2.1.10) \
• MCL (v22.282) \
• MMseqs2 (v15.6f452) \
• SeqKit2 (v2.9.0) (used only to build Pfam and AlphaFold databases)

LAGOON-MCL container (singularity) contains the Python modules. It is built from a container available on [Docker Hub] (https://hub.docker.com/r/jroussea/lagoon-mcl). The Dockerfile is available here.

# SeqKit2 v2.9.0
wget -O containers/seqkit/2.9.0/seqkit.sif https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0

# Diamond v2.1.10
wget -O containers/diamond/2.1.10/diamond.sif https://depot.galaxyproject.org/singularity/diamond:2.1.10--h43eeafb_2

# MCL v22.282
wget -O containers/mcl/22.282/mcl.sif https://depot.galaxyproject.org/singularity/mcl:22.282--pl5321h031d066_2

# MMseqs2 v15.6f452
wget -O containers/mmseqs2/15.6f452/mmseqs.sif https://depot.galaxyproject.org/singularity/mmseqs2:15.6f452--pl5321h6a68c12_3

# LAGOON-MCL v1.0.0
singularity build --fakeroot containers/lagoon-mcl/1.0.0/lagoon-mcl.sif docker://jroussea/lagoon-mcl:latest

Containers can be found in: containers/

Download and build databases

Before using LAGOON-MCL, it is necessary to download and build the Pfam and AlphaFold databases and convert them for use by MMseqs2.

cd tool-kit/

# Download Alphafold Protein Database [mandatory]
./build_alpahfold_db.sh

# Dowload Pfam [optional]
./build_pfam_db.sh

Databases are available in the database/ folder.

Cluster configuration

If you are using LAGOON-MCL on a computing cluster, you will need to provide Nextflow with a configuration file specific to your system. Information on executors (SLURM, PBS, AWS, ...) can be found in the executor section of the Nextflow documentation. For some institutes, this file is already referenced in nf-core/configs. If this is the case, you can download the file and use it with -c path/to/your/institute/config/file/institute_file.config when executing the pipeline.

Running the pipeline

nextflow run main.nf -profile test,singularity

For more information on running the pipeline, please see the tutorial.

Updating the pipeline

cd lagoon-mcl/
git pull

Usage

List of parameters is available here