2016 04 11 CyVerse Training Day - EMBL-ABR
Organizers: | V. Schneider, J. Williams |
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Local Point of Contact: | Christina Hall |
Trainers: | Jason Williams |
Date: | April 11, 2016 |
Location: | Lab-14 Seminar Space, VLSCI – The University of Melbourne 700 Swanston St (cnr Grattan St), Carlton, VIC 3053, Australia |
Required Workshop Prep
1. CyVerse Account
- Get your free account at http://user.iplantcollaborative.org/ . Please register with an institutional email account as only this will give you access to the CyVerse cloud service Atmosphere (see next bullet).
2. Atmosphere Access
- Once you have your account, go to http://user.iplantcollaborative.org/ and log in. Under "Apps and Services," scroll down to "Available Services" and request access to Atmosphere. Indicate that you are attending a workshop when you are asked for justification. (This will only be granted if you registered for CyVerse using an institutional account; see above.)
3. Laptop
Please bring your own WiFi enabled laptop to the workshop. Make sure your laptop has the following:
- Internet Browser: Please have an up-to-date web browser - We strongly recommend Firefox or Safari
- Data Store: Download and install iCommands (iCommands for your OS)
- VNC Viewer: Download the DMG (for MAC) or exe (for PC) (http://www.realvnc.com/download/viewer/)
- Windows Users only: Download and install PuTTY (http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html)
- Download Cyberduck: Using Cyberduck for Uploading and Downloading to the Data Store - Installing and Configuring Cyberduck
4. Pre-Workshop Guide and Homework
- Download and complete the exercises in the PRE-WORKSHOP PACKET to get the most out of the workshop.
- Complete this Pre-Workshop Survey
- Note (4/9): The wiki instructions for iCommands are not rendering properly. If you are setting up iCommands, you will need the following info when prompted.
Prompt | Entry |
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irodsHost | data.iplantcollaborative.org |
port | 1247 |
zone | iplant |
irodsUserName | your cyverse username |
Current iRODS password | your cyverse password |
Instructional Materials
You can download a copy of the workshop packet (CyVerse Toolkit) to follow along:
Workshop Program (DAY 1)
Time | Description | Toolkit | Slides | Tutorial | Links |
09:00 AM | Arrive / Sign-in / Setup Troubleshooting |
| Pre-Survey | ||
09:15 AM | Welcome - Presenter/Participant Self-Introductions | slides | PLOS Bioinformatics Competency Paper | ||
09:30 AM | Overview of the CyVerse | Getting Started with CyVerse | |||
09:45 AM | Managing "Big Data" using the CyVerse Data Store |
| slides | tutorial | Data Store Overview |
10:30 AM | Coffee Break |
| |||
10:45 AM | Navigate the CyVerse Discovery Environment (DE)
|
| slides | tutorial | |
11:15 AM | Workflows and HT-Jobs in the DE. |
| (p.17-18) | DE Manual on Workflows | |
12:00 PM | Lunch Provided |
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01:00 PM | DNA Subway (Workflows for Bioinformatics Education) | DNA Subway Website | |||
01:15 PM | Using the DE for RNA-Seq |
| slides | ||
01:45 | Stretch Break | ||||
02:15 PM | Atmosphere Cloud Computing |
| slides | tutorial | |
03:00 PM | Advanced CyVerse Applications |
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