TwoRunningModes

RseqFlow offers two run mode options. One is a simple unix shell run mode, the other is a VM workflow managed with Pegasus.

• Unix shell run mode
• VM workflow run mode

Unix shell run mode

This run mode targets the analysis of a small dataset or trial. All the code is integrated into unix shell scripts. All the required software is included in the download package and can be easily installed. There are four branches in RseqFlow, each of which is implemented as a separate command line shell script.

• Quality Control and SNP Calling
• Expression Level Quantification
• Differentially Expressed Gene Identification
• Alignment File Format Conversion

Each branch is run separately using a command line unix shell script.

• Download Unix shell run package
• Manual of Unix shell run mode

VM workflow run mode

This run mode manages the source code and the entire run process using Pegasus Workflow Management Service. It helps the workflow execute in different environments including desktops, campus clusters, grids, and clouds. Unlike the Unix run mode which is designed for small datasets, the VM workflow mode offers run management for large datasets. Pegasus is deployed in Virtual Machine, which exempts users from complex installation and configuration. If users want to use their own cluster without VM, they can simply use the VM as a submit machine for submitting jobs to the cluster. More details of the Pegasus VM workflow mode can be found in RseqFlow workflow .