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