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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  

Tip

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  • Unavailable Unavailable: App is disabled; may be outdated, unavailable due to maintenance.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 support@cyverse.org 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 https://de.cyverse.org/de/.

  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, and then click Launch Analysis. You will receive a notification and may close the Muscle App window.


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