ISMB/ECCB Tutorial and Demos

This page contains links and embedded tutorials for use at the 2015 Cyberinfrastructure session

Orientation and Discussion Questions

1. Get the iPlant username of your neighbor in the session
2. Use the etherpad to report your results: https://etherpad.mozilla.org/akes-ci-workshop

SAMPLE DATA

Download and unzip the following demo data for this workshop

• Sample data: Download (77MB)

Data Demo

Important Documentation

• Data Store Manual
• iDrop (Manual and Download links )
• iCommands (Manual and Download links)
  • Complete iCommands original docs (link)

Key Demo Functionalities

Page numbers refer to workshop packet on parent page

• iDrop Demo (p. 10-11)
• iCommands demo
• Creating Public links (p.11)
• Sharing Folders (p.12-13)
• Metadata and search (p. 32)
• Public Data Sharing (See http://mirrors.iplantcollaborative.org/)

Walk-through

1. Unzip a collection of images (sample data; local computer)
2. Upload the collection and verify the integrity of the upload (iDrop)
3. Add metadata to files (iDrop)

4. Upload an additional collection of images (iCommands)

   iput -rPVT local_directory/ iplant_directory

5. Generate and verify checksums (iCommands)

   ichecksum /iplant_directory

6. Synchronize a collection of files (iCommands)

   irsync -rV local_directory i: iplant_directory

7. Search for files by metadata (Discovery Environment)
8. Share a link to a file (Discovery Environment)
   1. Online documentation for public links
9. Share a collection with other iPlant users (Discovery Environment)
   1. Sharing within iPlant (Discovery Environment)

   2. Changing permission via iCommands

      Usage: ichmod [-rhvVM] null|read|write|own userOrGroup dataObj|Collection ...
       or    ichmod [-rhvVM] inherit Collection ...
       or    ichmod [-rhvVM] noinherit Collection ...
       -r  recursive - set the access level for all dataObjects
                   in the entered collection and subCollections under it
       -v  verbose
       -V  Very verbose
       -M  Admin Mode
       -h  this help
      Modify access to dataObjects (iRODS files) and collections (directories).

10. View publicly available data (Mirrors)
    1. Mirrors Site: http://mirrors.iplantcollaborative.org/browse/iplant/home/shared

RNA-Seq Demo

Important Documentation

• iPlant Learning Center - Full tutorial
• MAKER JBrowse tutorial
• MAKER publication
• GMOD MAKER tutorial

Key Demo Functionalities

Page numbers refer to workshop packet on parent page

• Launching analyses via GUI (Discovery Environment) - Workshop Packet (p.16-17)
• Analysis history and metadata
  • See DE Manual
• Visualization of alignments in Genome Browsers
  • Send to Genome Browser Link

Walk-through

• See iPlant Learning Center - Full tutorial

Atmosphere Cloud Compute Demo

Important Documentation

• See: Atmosphere User Manual

Key Demo Functionalities

Page numbers refer to workshop packet on parent page

• Launching and connecting to an instance (Atmosphere) see - Workshop Packet (p.23-24)

Walk-through

See iPlant Learning Center - Full tutorial

Agave API Demo

Reference Documentation

• See: Atmosphere User Manual

Key Demo Functionalities

• Transfer files using the API

Walk-through

See iPlant Github Page - iPlant Agave SDK