TERRA-REF Documentation
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Primary version
Primary version
  • Introduction
  • Scientific Objectives
  • Experimental Design
    • The Maricopa Agricultural Center (MAC)
    • Controlled Environment Phenotyping
    • Genomics
  • Data
    • How to Access Data
    • Data Products
      • Environmental conditions
      • Phenotype Data
      • Genomics data
      • Fluorescence intensity imaging
      • Geospatial information
      • Hyperspectral imaging data
      • Infrared heat imaging data
      • Meteorological data
      • Point Cloud Data
      • Controlled Environment phenotype data
    • Data Use Policy
    • Manuscripts and Authorship Guidelines
  • Protocols
    • Field Scanner
    • Sensor Calibration
    • Hyperspectral Data
    • Controlled Environment Protocols
    • Manual Field Data Protocols
    • Phenotractor Protocols
    • UAV Protocols
    • Genomic Protocols
  • Technical Documentation
    • Software
    • Data Standards
      • Existing Data Standards
      • Agronomic and Phenotype Data Standards
      • Genomic Data Standards
      • Sensor Data Standards
      • Data Standards Committee
    • Data Product Levels
    • Directory Structure
    • Data Transfer
    • Data Processing Pipeline
    • Time Series Data in Geostreams
    • Data Backup
    • Systems Configuration
  • Code of Conduct
  • Appendix
    • Glossary
    • Accessing BETYdb with GIS Software
  • References
  • Archived Documentation
    • Developer Manual
      • Submitting data to Clowder
      • Submitting data to BETYdb
      • Submitting Data to CoGe
      • Developing Clowder Extractors
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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. Archived Documentation
  2. Developer Manual

Submitting Data to CoGe

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Last updated 5 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