Home_Icon Learning Center Home

Launching an Analysis Job

When you are ready to analyze data, you can select from one of several hundred applications in the Discovery Environment. We will cover the minimum you need to launch an analysis using some sample data. In this example, we will use the Muscle multiple sequence aligner app, to align some DNA sequences.

Example Data

Input Description Example
Unaligned DNA sequence reads One or more sequences in FASTA format DE_sample_plants.fas

Discovery Environment App(s):

App name Version Description App link Notes/other links
Muscle 3.8.31 Multiple sequence aligner Muscle 3.8.31  


Applications in the Discovery Environment Apps menu have several features: de_app_icon

  • dots Dots: Show additional links including “App info”, “Add to Favorites”, and “Comments”.
  • info App Info: Information about the App including short description. user manual, number of successful analyses, date of last use, URL link to App
  • comment Comment: Add comments/feedback on the App
  • favorite Add to Favorite: Add to your list of favorite Apps
  • rating Rating: Rate the app, and see current community rating (may indicate how many others liked the App)
  • Unavailable Unavailable: App is disabled; may be outdated, unavailable due to maintenance. Contact for help using these
  • beta Beta: App is in beta testing (leave feedback if you use!)
  • private Private: Application is not public and not visible by all users

Example Discovery Environment Analysis: Multiple sequence alignment with MUSCLE

  1. If necessary, login to the

  2. Click apps_icon Apps from the DE workspace; search for MUSCLE 3.8.31 or click this link: Muscle 3.8.31. (Tip: when using the link in this guide, the Muscle app may start behind other open windows in the DE)

  3. Under “Analysis Name” leave the defaults or make any desired notes. muscle_app_window

  4. Under “Select Input data” click Browse, then navigate to and select DE_sample_plants.fas; then click OK.

    (Location: Community Data > cyverse_training > platform_guides > discovery_environment > muscle_3_8_31 > 01_muscle_input)

  5. Under “Sequence Type”, select DNA.

  6. Under Resource Requirements leave the default settings. If required, some analyses may be launched with requests for more resources, but this may cause those analyses to wait longer in the submission queue until a node that matches those minimum requirements becomes available.

  7. Click Launch Analysis. You will receive a notification and the Muscle App window will close.

Fix or improve this documentation