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Reproducibility Tour


Downloads, access, and services

In order to complete this tutorial you will need access to the following services/software

Prerequisite Preparation/Notes Link/Download
CyVerse account You will need a CyVerse account to complete this exercise CyVerse User Portal
Atmosphere access You must have access to Atmosphere CyVerse User Portal


We will use the following CyVerse platform(s):

Platform Interface Link Platform Documentation Quick Start
Data Store GUI/Command line Data Store Data Store Manual Data Store Guide
Discovery Environment Web/Point-and-click Discovery Environment DE Manual Discovery Environment Guide
Atmosphere Command line (ssh) and/or Desktop (VNC) Atmosphere Atmosphere Manual Atmosphere Guide

Application(s) used

Atmosphere Image(s):

Image name Version Description Link Notes/other links
Ubuntu 18.04 NoDesktop Base 2.0 Base image with Ubuntu 18.04 Atmosphere Image Large2 size recommended

Other Installations


In most cases, we will be installing these tools on Atmosphere instances. This tutorial is mostly command line. If using your own computer you will need a terminal already installed on Linux or mac). If you are using Windows, please see the instructions for installing the Windows Linux Subsystem.

Prerequisite Notes Links
Docker Docker is a technology for running individual software tools in a reproducible environment, and on any machine. We request you install The Desktop, Community Edition of Docker if you are using Windows or MacOS. The Docker CE x86_64 instructions are also available for Linux users. If you have installation problems, we will also have backup cloud instances available. Download Docker
Git Git is a version control software. If you are using Linux or MacOS, you most likely already have Git. Windows users may need to install Git. You can find instructions for Git installation at the link. Install Git
Text editor You will need to have a text editor suitable for working with code (Not Microsoft word, or other word processing software). We recommend Atom
Jupyter lab Jupyter is a popular data science workbench for reproducible analysis Install Juypyter lab
Windows Linux Subsystem (Windows PC only) This enables using Linux on Windows 10 PCs We suggested installing the Windows Linux Subsystem if you have a Windows 10 PC. Following the directions we also suggest installing an Ubuntu 18.04 LTS distribution.

Input and example data

In this tutorial, we will be assembling the genome of the protozoan Plasmodium falciparum - the parasite that causes malaria. We will be importing data from the NCBI Sequence Read Archive.

Input File(s) Format Preparation/Notes Example Data
NCBI Sequence read data NCBI SRA archival file Files will be imported using NCBI SRA tools NCBI Experiment Description

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