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

Discovery Environment Applications List

The box below searches only this space.
To search the entire iPlant wiki, enter your query in the box at the upper right.

Maintenance: Tues, 28 Jan 2020

ACCESS TO OR USAGE OF THE FOLLOWING SERVICES WILL BE UNAVAILABLE OR DISRUPTED:

Discovery Environment         8:00am to 5:00pm MST
The Discovery Environment will be unavailable while patches and updates are applied.
        ** Currently running analyses will be terminated. Please plan accordingly.

Data Store                    8:00am to 5:00pm MST
The Data Store will be unavailable during the maintenance period.
 
Data Commons                  8:00am to 5:00pm MST
The Data Commons will be unavailable during the maintenance period.
 
Atmosphere and Cloud Services 8:00am to 5:00pm MST
Marana Cloud: Atmosphere instances in the Marana Cloud will be operational; however, you will not be able to use the Data Store within your instance, and you may not be able to access the Atmosphere web interface.
 
User Portal                   8:00am to 5:00pm MST
The User Portal, http://user.cyverse.org, will be unavailable while we perform maintenance and updates.
 
Agave/Science API             8:00am to 5:00pm MST
The Agave/Science API will be unavailable during this maintenance period.
 
DNA Subway                    8:00am to 5:00pm MST
DNA Subway will be unavailable during this maintenance period.
 
The following services will NOT be affected by the maintenance: CyVerse Wiki and JIRA

Keep up to date with our maintenance schedules on the CyVerse public calendar
http://www.cyverse.org/maintenance-calendar
Check your local timezone here https://bit.ly/36iVOkX 
 
Please contact support@cyverse.org for any questions, or concerns.
 
Thank You,
CyVerse Staff 

 

 

 

 

 

 

Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

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.

Rationale and background:


Splitting a large file into a number of small lines based on line number is essential for many applications or analysis. This is especially useful if you have a long list of id's and then you want to use them parallelly using HT Analysis Path List file.

Pre-Requisites:

A CyVerse account (Register for a CyVerse account at https://user.cyverse.org).

An up-to-date Java-enabled web browser. (Firefox recommended. If you wish to work with your own large datasets and upload them using iCommands, Chrome is not suitable due to its issues in utilizing 64-bit Java.)

Mandatory arguments

  1. Inputs
    1. Input File: Path to the input file that contains the list of id's
    2. Number of lines per file: How many lines that you want to split the input file into. The number of output files corresponds tonumberof lines that you want to split into
    3. File_prefix: Prefix of the file that gets created (Default is "x")
  2. Outputs
    1. Output folder: Name of the output folder (Default is "Output")

Test run

The test data for this app is located at /iplant/home/shared/iplantcollaborative/example_data/OSG-RMTA/sra_id_list.txt
The 'sra_id_list.txt' file contains a list of 15 SRA id's, one SRA ID per line

 

Code Block
SRR3403881
SRR5227388
SRR5227389
SRR5227390
SRR5227391
SRR5227392
SRR5227393
SRR5227394
SRR5227395
SRR5227396
SRR5227397
SRR5227398
SRR5227399
SRR5227400
SRR5227401
  1. Inputs
    1. Input File: /iplant/home/shared/iplantcollaborative/example_data/OSG-RMTA/sra_id_list.txt
    2. Number of lines per file: 5
    3. File_prefix: osg_rmta_
  2. Outputs
    1. Output folder: OSG-RMTA-File-Split

After a successful run, you'll get 3 files each containing 5 SRA Id's with the prefix osg_rmta_ in OSG-RMTA-File-Split folder