Parallel execution of pipelines using bioinformatics tools

• Main Author: Fleitas, Calmenelias Pino
• Publication Date: 2019
• Format: Master thesis
• Language: eng
• Source: Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
• Download full: http://hdl.handle.net/10400.21/12436
• topic: NGSPipes; Pipeline; Fluxo de trabalho; Execution; Execução; Tool metadata.; Metadados das ferramentas

The project “Parallel execution of pipelines using bioinformatic tools”, from now on referred to as NGSPipesV2, is part of a platform that allows the creation and execution of pipelines (set of tools to execute). NGSPipesV2 extends the project “Infrastructure to support the execution of workflows for bioinformatics”, from now on referred to as NGSPipesV1. NGSPipesV1 project was developed within the final project of the Licenciatura em Engenharia Informática e de Computadores (LEIC) of Instituto Superior de Engenharia de Lisboa (ISEL). The main goal of both projects is to help the scientific community to perform biological data processing using Next Generation Sequencing (NGS) techniques. For this purpose, both NGSPipes projects supports the creation and execution of pipelines (e.g. sequences of tasks), avoiding scientists to solve problems like installing tools and their dependencies and write scripts in order to execute pipelines. NGSPipesV2 extends NGSPipesV1 with the main objectives of adding support for the parallel execution of pipelines, orchestrate the execution of pipelines in remote clusters and improve the expressiveness of metadata for tools annotation.