customized cloud platform for computing on your terms !
TRANSCRIPT
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Customized cloud platform for computing on your terms !
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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
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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
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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)
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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
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• 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
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Atmosphere: Collaboration
iPlant Data Store
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Lifecycle
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How to Connect
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Different Ways to Log in to VMs
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Run the Integrative Genome Viewer
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Accessing Your Virtual Machine• VNC client• Command line tools (e.g. SSH)
www.realvnc.com
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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
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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/
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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
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Import Needed Data using DE
Step 1: click icon “Import from URL”Step 2: Paste URL’s & click “Upload”
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Log In to Atmosphere(One member of team)
https://atmo-beta.iplantcollaborative.org/login/
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Launch AtmosphereSelect “NGS Viewers” Takes 10-15 min: you will receive e-mail
notification with needed IP address
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Launch Atmosphere• Confirmation message• Can take 10-15 min to complete request• You will receive e-mail notification with needed IP address
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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
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Launching VNC
Paste your DNS (IP address)Add “:1” to end
Enter iPlant Username & Password
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Moving Data with iDrop
Right click on iDrop icon and select “Open”
*Do not click icon multiple times!
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Log In to iDropAtmosphere: Moving Data w/ iDrop
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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
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Sharing Your Atmosphere Instance Step 1Open “VNC Server (User-Mode) or click icon
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Sharing Your Atmosphere Instance Step 2
Click “Configure”
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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
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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)
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Load Arabidopsis v10 Genome
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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
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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
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Terminate Your Instance!Final Step…
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https://pods.iplantcollaborative.org/wiki/display/atmman/Getting+Help+and+Asking+Questions#https://forums.iplantcollaborative.org/
Thank you!