Bioinformatics Specific Options

  • We prepared machine images equipped with elasticHPC and a set of pre-installed bioinformatics tools that can be directly accessed upon the creation of the cluster.
  • We also prepared EBS volumes and public S3 directory with a set of databases.
  • We integrated web-interface for the installed bioinformatics tools to facilitate the use of cloud services.

Preconfigured machines for Bioinformatics

Currently, there are about 200 tools, coming from BioLinux, SAMtools , fastx , NCBI BLAST Toolkit, and other individual sequence analysis programs that run on traditional machines and MapReduce. The details of these tools are given below. Addition of extra tools and updating this image is explained in this part of the manual (click here). The available tools belong to the following packages:

  • Sam Tools
  • FASTX-Toolkit
  • MAQ
  • Bowtie
  • BWA
  • BFast
  • Clustalw2
  • T-Coffee
  • Crossbow

Biological databases

To save user’s cost and to facilitate usage of database-dependent programs, we prepared snapshots of different databases. These snapshots are made available to the user free of charge through a simple user interface, to create EBS volumes and mount them to the cluster. Our snapshots currently include the sequence databases and pre-computed indexes of it to be used with the respective tools.

List of snapshots

To list of the all the snapshots and its content Click Here

Cloud based web-server

To facilitate the use of elastiHPC, we augmented the cloud machines with web-interface to

  • run any of the pre-installed software tools.
  • upload executable program of choice and run it on the cloud infrastructure.

Web-interface for Pre-installed tools

There is a tools reprosotary that allows the user to submit jobs for the pre-installed called ‘NUBIOS’, NUBIOS can be accessed on: ‘http://MAIN_NODE_DNS/NUBIOS

Web-interface of generic tool

If the user wants to run a tool that doesn’t exist currently on the cluster, you can use our tool runner page ‘http://MAIN_NODE_DNS/runner‘ which allows you to fetch the tool binary, input files from local cluster or S3.