Prerequisites

  • Software (required)

    • Linux system (tested: CentOS 7)

    • MariaDB database

    • BLAST

    • IgBLAST

    • Muscle

    • RazerS

    • Perl with BioPerl

    • R with BioConductor (flowcore package)

  • Software (recommended for pre-processing)

    • PandaSeq

  • Configuration

    • MariaDB user account with complete database access

    • .my.cnf file holding the credentials

Basic Setup for a project

It is recommended to keep all data for a specific project within one directory and one corresponding database scheme. Each project directory contains its individual version of the sciReptor code, this was done to make projects independend from each other in terms of code updates. To implement an easy way for updates it is recommended to clone the current version of the sciReptor git repository instead of just copying the script files. It is shown below how to do this.

The config file contains all information that is required for data processing. It does not contain any metadata, although some fields (e.g. species) will overlap with the metadata files.

  • Database: The pipeline requires a Database, i.e., an instance of the sciReptor database schema [link database chapter] provided by a MariaDB 5.5 instance. The user running the processing needs full access to this Database.

  • Library: The reference library to be used by Blast and RazorS