Wednesday
BACK: 2015 Main Page
JOINME: https://join.me/bioinfosu
Lecture: Introduction to iPlant -- Peter Hoyt (8:30-9:30)
Slides: https://drive.google.com/file/d/0BwLI3KMs2RkrVmZxVU8yWk5KSEk/edit?usp=sharing
- Lecture – The iPlant Discovery Environment and Data Store
- Login and Directory structure
- Opening and using Apps
- Saving and Managing Data
Hands on exercises: https://drive.google.com/file/d/0BwLI3KMs2RkrSXI5VE5uZnZWNkE/edit?usp=sharing
- Downloading Sequence Data From NCBI
- Signing Into The Discovery Environment and Simple Uploads
- Using Apps in the Discovery Environment
- Installing and Using iDROP https://code.renci.org/gf/project/irodsidrop/frs
- Performing Quality Control on Sequence Data
- (Optional) Fixing datafiles
- (Optional) BlastX of clean data on Cowboy
Links to original .SRA Files:
http://de.iplantcollaborative.org/dl/d/2556CA45-42D0-43FC-8EE5-640B8267398A/SRR023845.sra
http://de.iplantcollaborative.org/dl/d/8030CD45-241B-4F82-A76B-78B4221D7F22/SRR023846.sra
OR
ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR023/SRR023845/SRR023845.sra
ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR023/SRR023846/SRR023846.sra
The iPlant Atmosphere
Lecture: The iPlant Atmosphere -- Peter Hoyt (9:30 - 11:00)
Slides: https://drive.google.com/file/d/0BwLI3KMs2RkrUHNma2ZpZk1mNzA/edit?usp=sharing
- About Instances
- Creating NEW Instances
- Mounting a volume and creating a file system
- Accessing your Instance
- Using Shell
- Using VNC
- Using Putty
- Restoring data from the Data Store
- iCommands
Hands on exercise: https://drive.google.com/file/d/0BwLI3KMs2RkrVlNvdy1SbmNibFU/edit?usp=sharing
- Starting a new instance (Use 5 groups)
- Creating a new volume
- Attaching, mounting and putting filesystem on new volume
- Connecting to your Atmosphere Instance
- Shell
- Putty
- VNC on Chrome
- Using iCommands
- for complete instructions read: https://wiki.irods.org/index.php/icommands
- Creating folders and files with VNC
- Sharing your VNC Shession
(Early) Lunch (11:00-11:45)
JOINME: https://join.me/bioinfosu
Lecture: CoGe - Eric Lyons - iPlant (12:00 - 5:00)
- Lecture slides and links to data used in hands-on: CoGe
Break (2:30-2:45) (optional)
Hands-On:
CoGe Exercises: https://docs.google.com/document/d/1H2d1d9cp35ajLu-IlN_dnLEqBKjIWZOHPzoTW4Qek6s/edit?usp=sharing