Customized cloud platform for computing on your terms !
What is cloud computing ?
http://geekandpoke.typepad.com/geekandpoke/2009/03/let-the-clouds-make-your-life-easier.html
The practice of using a network of remote servers hosted on the Internet to store, manage, and process data
What is Atmosphere?• On-demand computing resource built on a cloud
infrastructure• Virtual Machine pre-configured with:
– Software– Memory requirements– Processing power
• Fully integrated into iPlant authentication and storage and HPC capabilities
• Enables users to build custom images/appliances and share with community
• Cross-platform desktop access to GUI applications in the cloud (using VNC)
• Provide easy web based access to resources
Atmosphere: motivation• Standalone GUI-based applications are frequently
required for analysis but not easy to transform into web apps
• Need to handle complex software dependencies (e.g specific bioperl version and R modules)
• Users needing full control of their software stack (occasional sudo access)
• Need to share desktop/applications for collaborative analysis (remote collaborators)
Who is this tutorial designed for ?
• Users wanting to launch configured images in atmosphere (like app store)
• Developers for application distribution• Prototyping/Testing new software/modules• Tailored software training setups (custom
workshops/laboratory courses etc)• Extend compute capabilities of existing
applications i.e. utilize iPlant API
• API-compatible implementation of Amazon EC2/S3 interfaces
• Virtualize the execution environment for applications and services
• Up to 12 core / 48 GB instances• Access to Cloud Storage + EBS• >60 hosted applications in Atmosphere
today, including users from USDA, Forest Service, database providers, etc.
The iPlant CollaborativeProject Atmosphere™: Custom Cloud Computing
Atmosphere: Collaboration
iPlant Data Store
Lifecycle
How to Connect
Different Ways to Log in to VMs
Run the Integrative Genome Viewer
Accessing Your Virtual Machine• VNC client• Command line tools (e.g. SSH)
www.realvnc.com
Atmosphere Exercise Objectives
• Launch an Atmosphere VM, “NGS Viewers”• Connect using VNC Viewer• Move data using iDrop• Share instance with selected users• Launch IGV “Integrative Genomics Viewer”• View RNA-seq alignments to Arabidopsis
reference genome• TERMINATE YOUR INSTANCE WHEN DONE
Additional On-line Instruction• Atmosphere Manual:
https://pods.iplantcollaborative.org/wiki/display/atmman/Table+of+Contents
• iDrop: https://pods.iplantcollaborative.org/wiki/display/start/Using+iDrop
• IGV: http://www.broadinstitute.org/igv/UserGuide
• RealVNC: https://www.realvnc.com/
Atmosphere Exercise Preparation
• Work in teams of 4– One person in team will launch Atmosphere & share
with other team members• Download and Install VNC Viewer
– https://pods.iplantcollaborative.org/wiki/display/atmman/Using+VNC+to+Connect+to+an+Atmosphere+VM
• Import required data files to your home directory– http://data.iplantcollaborative.org/quickshare/ca5fe5d6defaec8e/W
T_rep1.fastq.tophat.bam
– http://data.iplantcollaborative.org/quickshare/b4bd99ee1ec54b6a/WT_rep1.fastq.tophat.bam.bai
Import Needed Data using DE
Step 1: click icon “Import from URL”Step 2: Paste URL’s & click “Upload”
Log In to Atmosphere(One member of team)
https://atmo-beta.iplantcollaborative.org/login/
Launch AtmosphereSelect “NGS Viewers” Takes 10-15 min: you will receive e-mail
notification with needed IP address
Launch Atmosphere• Confirmation message• Can take 10-15 min to complete request• You will receive e-mail notification with needed IP address
View Status in Dashboard
Status “pending” will change to “running”You will also get an e-mail notification with IP address
IP Address needed to log into VNC
Launching VNC
Paste your DNS (IP address)Add “:1” to end
Enter iPlant Username & Password
Moving Data with iDrop
Right click on iDrop icon and select “Open”
*Do not click icon multiple times!
Log In to iDropAtmosphere: Moving Data w/ iDrop
Atmosphere: Moving Data w/ iDrop
• Navigate to files in your iRods Data Store• Navigate to your Atmosphere Home Directory• Drag Files to copy:
• WT_rep1_fastq.tophat.bam• WT_rep1_fastq.tophat.bam.bai
Sharing Your Atmosphere Instance Step 1Open “VNC Server (User-Mode) or click icon
Sharing Your Atmosphere Instance Step 2
Click “Configure”
Sharing Your Atmosphere Instance Step 3
1. Click “Add User”2. Enter iPlant User Name you
wish to share with3. Click “Add User” AGAIN! 4. “OK”
• Give Users the IP Address needed to Log In
• Shared Users can launch VNC, login, and share the desktop
Launch Integrative Genomics Viewer• IGV is desktop application for customized Genome Browsing• Many pre-installed genomes (or can load your own genome)• Upload and view your own annotations & experimental data• Many file formats accepted (e.g. BAM, GFF, BED)
Load Arabidopsis v10 Genome
Load Expression Data From File
Load From File: ”WT_rep1.fastq.tophat.bam”
WT_rep1.fastq.tophat.bam.bai must be in same directory but is not loaded directly
IGV View RNA-seq Alignment Tracks
• Need to zoom in and navigate around to find aligned regions• Good Example Chr1:4,560,423-4,568,773• Or enter gene of interest• Tracks show stacked alignment and bar-graph
Terminate Your Instance!Final Step…
https://pods.iplantcollaborative.org/wiki/display/atmman/Getting+Help+and+Asking+Questions#https://forums.iplantcollaborative.org/
Thank you!