The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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The CyVerse App Store is currently being restructured, and apps are being moved to an HPC environment. During this transition, users may occasionally be unable to locate or use apps that are listed in our tutorials. In many cases, these apps can be located by searching them using the search bar at the top of the Apps window in the DE. To increase the chance for search success, try not searching the entire app name and version number but only the portion that refers to the app's function or origin (e.g. 'SOAPdenovo' instead of 'SOAPdenovo-Trans 1.01').

Also, as part of the 2.8 app categorization, a number of apps were deprecated and are no longer available, and there is no longer an Archive category. You can search for a suitable replacement in the List of Applications in this window, or search on an app name or tool used for an app in the Apps window search field. If you need an app reinstated, please contact support@cyverse.org.


The DE Quick Start tutorial provides an introduction to basic DE functionality and navigation.

Please work through the tutorial and add your comments on the bottom of this page. Or send comments per email to support@cyverse.org. Thank you.

This app can be used to run Cufflinks-2.2.1 using SAM files instead of BAM files. This app is basically a workflow that consists of two apps

 

Pre-Requisites

  1. A CyVerse account. (Register for an CyVerse account here - user.cyverse.org)
  2. Input file(s)
    1. Input file Name: SAM files generated from any mapper
  3. Output
    1. Output File name: Name of the output file (output.sorted.bam is default)
  4. Cufflinks-2.2.1: Regarding parameters for this section, please refer to Cufflinks-2.2.1

     

Test/sample data

The test data for testing QUAST in here : /iplant/home/shared/iplantcollaborative/example_data/Samtools-SAMtoSortedBAM

Test run

  1. Input file: BowtieOutput.sam
  2. Output: Default file name
  3. Cufflinks-2.2.1: Leave everything default

Test Results

Successful execution of the QUAST assessment pipeline will create the following files and folders:

  1. logs
  2. output_out: This folder contains cufflinks related outputs (genes.fpkm_tracking, isoforms.fpkm_tracking, skipped.gtf and transcripts.gtf)
  3. output.sorted.bam
  4. output.sorted.bam.bam.bai

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