CyVerse Austria Workshop¶

Location: Technical University of Graz Lehrsaal VI (FS EG 076) Inffeldgasse 11 (with TUG Wifi)

This “Train-the-trainer” style workshop will be a week-long collaboration between CyVerse trainers and staff from CyVerse US as well as trainers and staff from CyVerse Austria. Over the week, the goal will be to help each CyVerse Austria trainer:

Know the basic capabilities of CyVerse Austria infrastructure
Give feedback to shape the development of CyVerse Austria infrastructure
Be able to customize and install tools required by CyVerse Austria users
Develop effective training and documentation skills to make CyVerse Austria a success for its users.

Currently, the CyVerse Austria cyberinfrastructure implements key capabilities of CyVerse infrastructure:

Data Store: Data storage, sharing, metadata management,
Discovery Environment: A web-based, graphical interface to hundreds of bioinformatics tools
Visual and Interactive Computing Environment: Jupyter labs, RStudio, and RShiny applications easily launched and managed in the Discovery Environment

Pre-Workshop Setup¶

Minimum Setup Instructions

We ask that all attendees download/install the following software tools prior to the workshop. If you have any difficulty, we will have time to help you with installation problems during the workshop.

Hardware/Software

Prerequisite	Notes	Links
Wi-Fi-enabled laptop (Mac or Linux recommended)	You should be able to use CyVerse from any laptop using Windows/MacOS/Linux. We Strongly recommend having access to a laptop running Windows/MacOS. While you will be able to use CyVerse components from any laptop, some of the tool installations may work better with those operating systems. If you are using Windows, you may wish to install Linux Bash for Windows. We also strongly recommend Firefox or Chrome browser; We do not recommend Microsoft Edge Browser. It is helpful if you have administrative/install permissions on your laptop. Note: If specified, some workshops will be held in computer labs in which case a laptop is optional.	Download FireFox Download Chrome
Cyberduck	Cyberduck is a third-party tool for uploading/downloading data to CyVerse. Currently, this tool is available for Windows/MacOS only. You will need to download Cyberduck and the connection profile. We will go through configuration and installation at the workshop.	Download Cyberduck
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 installing Atom
Python (optional)	For our documentation you will need Python 3 (3.8.0 or later) installed. this is likely already installed on Linux/MacOS systems	Install Python
Python package manager PIP (optional)	For our documentation you will need Python 3 (3.8.0 or later) installed	Install Python PIP
Python sphinx (optional)	For our documentation you will need sphinx and themes	# run this command at the terminal $ pip install sphinx $ pip install sphinx-autobuild $ pip install sphinx_rtd_theme
Python RestView (optional)	For our documentation RestView documentation.	# run this command at the terminal $ pip install restview

Accounts

Prerequisite	Notes	Links
CyVerse Austria Account	Please ensure you have a CyVerse account and have verified your account by completing the verification steps in the email you got when you registered. You can test your account by logging into CyVerse Austria User Portal.	Register for your CyVerse account at CyVerse Austria User Portal. Please register using an institutional email address (e.g. .edu/.gov/.org etc.).
Github	We will make use of Github for managing documentation, and also any software/scripts developed (E.g. Docker files).	Register for a GitHub account
Dockerhub	Dockerhub is an online repository for the sharing and management of Docker images.	Register for a Dockerhub account
University VPN	If you want to access data located at your home institution, you may want to have VPN (virtual private network) software installed.	Contact your university IT department if you need assistance.

Optional and Extras

These are some extra steps that aren’t required for the workshop, but which provide some options for functionalities we will cover.

Tool	Notes	Link
VNC Viewer	This tool enables connection to a remote Atmosphere Desktop. No installation or configuration is needed.	Download VNC Viewer
PuTTY (windows only)	PuTTY allows SSH connection to a remote machine, and is designed for Windows users who do not have a Mac/Linux terminal.	Download PuTTY
iCommands	iCommands are third-party software for command-line connection to the CyVerse Data Store.	Download and installation instructions available at CyVerse Learning Center - iCommands

Slack¶

We will Slack for shared notes and easy exchange of code, feedback, links, etc.: TBA

Important links¶

CyVerse Austria User Portal: https://user.cyverse.tugraz.at/
CyVerse Austria Discovery Environment: https://de.cyverse.tugraz.at/
CyVerse Austria Data Store configuration:
- irods host: data.cyverse.tugraz.at
- irods zone: TUG
- irods port: 1247
Instant Session Feedback: Feedback form

Agenda¶

This workshop is will be interactive and collaborative (part training workshop, part coda-a-thon/hack-a-thon). For the most part, mornings will start with some lectures, discussion, and hands-on exercises. We will then decide as a group what the afternoon agenda should focus on. We also anticipate that attendees may want to different things and we will have some capacity to divide into smaller groups. Everything on the agenda is up for discussion, if something you would like to see is missing we can add it!