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 documentation and add your comments on the bottom of this page, or email comments to support@cyverse.org. Thank you.

Rationale and background

unpigz-2.3.4 (Parallel Implementation of Gzip) is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when uncompressed


Pre-Requisites

  1. A CyVerse account. (Register for an CyVerse account here - user.cyverse.org)
  2. Mandatory arguments 
    1. Input - One or more files that needs to be uncompressed
    2. Output folder - Name of the output folder where the compressed files will be placed
  3. Optional Parameters:
    1. Compress faster : Indicates the fastest uncompression method (less compression)
    2. Compress better : indicates the slowest uncompression method (best compression)

Test/sample data

The following test data are provided for testing HISAT2 in here - /iplant/home/shared/iplantcollaborative/example_data/uncompress_files_with_gunzip:

  1. trin10.fa.gz
  2. trin11.fa.gz

Results 

Successful execution of the  unpigz will create a directory named Output. The directory will contain uncompressed file or files

Output

  1. trin10
  2. trin11

 

Icon

pigz-2.3.4 manual - http://zlib.net/pigz/

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