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Requirements

Cluster Flow is designed to work with a computing cluster. It currently supports the Sun GRIDEngine, LSF and SLURM job managers (not PBS, Torque or others).

If you don't have a cluster with a supported manager, you can run Cluster Flow on any command-line machine in local mode. This writes a bash script and runs it as a job in the background.

To run analyses, you will also need the required tools to be installed. Cluster Flow is designed to work with the environment module system and load tools as required, but if software is available on the PATH it can work without this.

Cluster Flow itself is written in Perl. It has minimal dependencies, all of which are core Perl packages.

Environment Module

If you are a user on a HPC cluster, you may already have Cluster Flow installed on your cluster as an environment module. If so, you may be able to load it using:

module load clusterflow

Manual Installation

Cluster Flow is a collection of stand-alone scripts, mostly written in Perl.

  1. Download Cluster Flow (see the releases page)
wget https://github.com/ewels/clusterflow/archive/v0.5.tar.gz
  1. Extract the files
tar xvzf v0.5.tar.gz
  1. Create & configure the site-wide configuration file
cd clusterflow-0.5
cp clusterflow.config.example clusterflow.config
vi clusterflow.config

You must specify your environment in the config file (@cluster_environment: local, GRIDEngine, SLURM or LSF), most other things are optional.

The cf executable must be in your system PATH, so that you can run it easily from any directory. Ensure that you run the Configuration Wizard (described below) so that this config is created in your ~/.bashrc file.

If you prefer, you can symlink the cf executable to ~/bin.

Configuration Wizard

Once Cluster Flow has been set up site-wide, you need to configure it for your personal use:

cf --setup

This will launch a wizard to write a config file for you, with details such as e-mail address and notification settings.

Adding Reference Genomes

Most analysis pipelines need a reference genome. This can exist in a central location or in your personal setup (or both).

If you're using the Swedish UPPMAX cluster, please see these instructions.

You can add your reference genome paths with the following wizard:

cf --add_genome

Do a test run!

That should be it! Log out of your session and in again to activate any new bash settings. Then try launching a test run:

cf --genome GRCh37 sra_bowtie ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/SRX/SRX031/SRX031398/SRR1068378/SRR1068378.sra

This will download SRR1068378 (Human H3K4me3 ChIP-Seq data), convert to FastQ, run FastQC, Trim Galore! and align with bowtie.