Introduction to CyVerse¶
Goals¶
Introduce NEON scientists and staff to CyVerse and its resources.
Demonstrate via hands-on exercises the CyVerse Data Store, Data Science Workbench (Discovery Environment), Cloud (Atmosphere), BisQue image analysis, Data Commons, and Powered By features.
Open discussion about how NEON staff or academic scientists working with NEON data could begin to utilize CyVerse at scale.
Suggested topics:
- Identify NEON’s computational and data storage|sharing bottlenecks that CyVerse can ameliorate.
- Identify missing components from the current CyVerse infrastructure that NEON requires.
Prerequisites¶
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 | Register |
| Atmosphere access | You must have access to Atmosphere | Request Access |
| CyVerse Data Store allocation increase (Optional) | You must be registered for CyVerse | Request Increase (form #2) |
| Jetstream access (Optional) | You must have registered with XSEDE | Request Access |
| Cyberduck (Optional) | Standalone program for uploading/downloading data to Data Store | Download |
| Windows 10 Linux Subsystem (Optional) | Install Ubuntu Bash on a Windows OS | Installation Instructions |
| iCommands Installation (Optional) | Install iCommands for Linux, Windows, or Mac OSX | Installation Instructions |
Platform(s)¶
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 |
| BisQue | Web/Point-and-click and/or Command-line (API) | BisQue | BisQue Manual | (See Manual) |
| DNA Subway | Web/Point-and-click | DNA Subway | (See Guide) | DNA Subway Guide |
| SciApps | Command-line (API) | SciApps | (See Guide) | SciApps Guide |
| Agave API | Command-line (API) | Agave API | Agave Live Docs | Agave Guide |
Application(s) used¶
Discovery Environment App(s):
| App name | Version | Description | App link | Notes/other links |
|---|---|---|---|---|
| Muscle | 3.8.31 | Multiple sequence aligner | DE Application URL | Original App Documentation |
| Jupyter-Lab | 0.0.3 | Base Jupyter Lab Image | VICE Application URL | VICE Manual |
| RStudio Geospatial | 3.5.0 | Based on Rocker Geospatial RStudio Image | VICE RStudio URL | Rocker Docker |
| Shiny Apps | 1.5.9 | R Shiny with Geospatial dependencies (GDAL, GEOS, etc) | Geospatial Shiny App | Rocker Shiny |
Atmosphere Image(s):
| Image name | Version | Description | Link | Notes/other links |
|---|---|---|---|---|
| CyVerse CentOS 6.8 GUI Base | 1.0 | base image CentOS 6.8 with GNOME GUI | Atmosphere Image 1 | |
| Ubuntu 18.04 GUI XFCE Base | 1.0 | base Ubuntu 18.04 with GNOME GUI | Atmosphere Image 2 |
Input and example data¶
In order to complete this tutorial you will need to have the following inputs prepared
| Input File(s) | Format | Preparation/Notes | Example Data |
|---|---|---|---|
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