TERRA-REF Documentation
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  • Introduction
  • Data Sources
  • Software
  • Scientific Objectives and Experimental Design
    • Protocols
      • Controlled Environment Protocols
      • Manual Field Data Protocols
      • Phenotractor Protocols
      • Sensor Calibration
      • Template Protocol
      • UAV Protocols
    • Experimental Design
      • Experimental Design Danforth
        • Sorghum Lines Danforth
      • Experimental Design Genomics
        • Sorghum Lines Genomics Year 1
        • Sorghum Lines Genomics Year 1 (continued)
        • Sorghum Lines Genomics Year 2
      • Experimental Design MAC
  • User Manual
    • What Data is Available
    • Data Products
      • Environmental conditions
      • Fluorescence intensity imaging
      • Genomics data
      • Geospatial information
      • Hyperspectral imaging data
      • Infrared heat imaging data
      • Multispectral imaging data
      • Meteorological data
      • Phenotype data
      • Point Cloud Data
    • How to Access Data
      • Using Clowder (Sensor and Genoomics data)
      • Using Globus (Sensor and Genomics data)
      • Using BETYdb (trait data, experimental metadata)
        • Accessing BETYdb via ArcMap and other GIS software
      • Using CoGe (Genomics)
      • Using CyVerse (Genomics)
      • Using Analysis Workbench (all data)
    • Data Use Policy
    • Manuscripts and Authorship Guidelines
    • Release / reprocessing schedule
  • Technical Documentation
    • Data Standards
      • Existing Data Standards
      • Agronomic and Phenotype Data Standards
      • Genomic Data Standards
      • Sensor Data Standards
      • Data Standards Committee
    • Directory Structure
    • Data Storage
    • Data Transfer
    • Data Processing Pipeline
      • Geospatial Time Series Structure
    • Data Backup
    • Data Collection
    • Data Product Creation
      • Genomic Data
      • Hyperspectral Data
    • Quality Assurance and Quality Control
    • Systems Configuration
  • Developer Manual
    • Submitting data to Clowder
    • Submitting data to BETYdb
    • Submitting Data to CoGe
    • Developing Clowder Extractors
  • Tutorials
  • Appendix
    • Code of Conduct
    • Collaboration Tools
    • Glossary
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  • Submitting Sequences to the CoGe Pipeline
  • CyVerse data store
  • Uploading data to data store using icommands
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  1. Developer Manual

Submitting Data to CoGe

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Last updated 7 years ago

supports the genomics pipeline required for the TERRA program for Sorghum sequence alignment and analysis. It has a web interface and REST API. CoGe is developed by Eric Lyons and hosted at the University of Arizona, where it is made available for researchers to use. CoGe can be hosted on any server, VM, or Docker container.

Submitting Sequences to the CoGe Pipeline

  • Upload files to Cyverse data store. The TERRARef project has a 2TB allocation

  • Use icommands to transfer to data store

CyVerse data store

  • project directory: /iplant/home/shared/terraref

    • Raw data goes in subdirectory raw_data/, which is only writable for those sending raw reads.

  • (CoGe output) can go into output/

Uploading data to data store using icommands

Transferring data from Roger to iplant data store

# install icommands
cd $HOME
mkdir bin
cd bin
wget http://www.iplantcollaborative.org/sites/default/files/irods/icommands.x86_64.tar.bz2
tar -xvf icommands.x86_64.tar.bz2
# add icommands directory to $PATH
export PATH=$HOME/bin/icommands:$PATH
# initialize
iinit
# host name: data.iplantcollaborative.org
# port number:1247
# user name:(your Cyverse Login)
# Enter your irods zone:iplant
# iRODS password:*******
icd /iplant/home/shared/terraref/raw_data/hudson-alpha/
## transfer test data to iplant data store
touch checkpoint-file
iput -P -b -r -T --retries 3 -X checkpoint-file test_data/
CoGe
icommands documentation