SCBI_MapReduce, a New Ruby Task-Farm Skeleton for Automated Parallelisation and Distribution in Chunks of Sequences: The Implementation of a Boosted Blast+

Abstract

Current genomic analyses often require the managing and comparison of big data using desktop bioinformatic software that was not developed regarding multicore distribution. The task-farm SCBI_M AP R EDUCE is intended to simplify the trivial parallelisation and distribution of new and legacy software and scripts for biologists who are interested in using computers but are not skilled programmers. In the case of legacy applications, there is no need of modification or rewriting the source code. It can be used from multicore workstations to heterogeneous grids. Tests have demonstrated that speed-up scales almost linearly and that distribution in small chunks increases it. It is also shown that SCBI_M AP R EDUCE takes advantage of shared storage when necessary, is fault-tolerant, allows for resuming aborted jobs, does not need special hardware or virtual machine support, and provides the same results than a parallelised, legacy software. The same is true for interrupted and relaunched jobs. As proof-of-concept, distribution of a compiled version of B LAST+ in the SCBI_D ISTRIBUTED _B LAST gem is given, indicating that other blast binaries can be used while maintaining the same SCBI_D ISTRIBUTED _B LAST code. Therefore, SCBI_M AP R EDUCE suits most parallelisation and distribution needs in, for example, gene and genome studies.