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make.sh
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#!/bin/bash
#
# RO manager script to test RO for features in Y2 review demo
#
source ../../ro.sh
TESTRO="."
RONAME="soapdenovo-v2"
echo "--------"
$RO config -v \
-b $ROPATH \
-r "http://sandbox.wf4ever-project.org/rodl/ROs/" \
-t "3c7483ac-e157-4cb3-97d5-8cf6e129f8e9" \
-n "Jun Zhao" \
-e "[email protected]"
# ro config \
# -b /Users/graham/Desktop/robase \
# -r "http://sandbox.wf4ever-project.org/rodl/ROs/" \
# -t "32801fc0-1df1-4e34-b" \
# -n "Test user" \
# -e "[email protected]"
# -b /Users/graham/Desktop/robase \ # base directory for ROs
# -r "http://sandbox.wf4ever-project.org/rodl/ROs/" \ # URI for ROSRS service used for ro push, checkout
# -t "32801fc0-1df1-4e34-b" \ # Auth bearer token for ROSRS access
# -n "Test user" \ # User name
# -e "[email protected]" # User email
# Remove old RO structure
rm -rf .ro
# show simple directory content
ro create "RO for SOAPdenovo case study" -d . -i $RONAME
# add all files from currenmt directory to RO
ro add -a -d .
# Show aggregated files
ro list -d .
# Basic information about the RO
ro annotate . dcterms:descriptions "RO that aggregates the ISA documents, the nanopublication statements as well as information about the workflow used to produce the results."
# Aggregate the ISAOWL and Nanopublication statements by links
ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/isatab_distribution/1
ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/isaowl_distribution/1
ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/study/1
ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/nanopub/1/
ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/nanopub/2/
ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/nanopub/3/
ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/nanopub/4/
ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/nanopub/5/
ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/nanopub/6/
ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/nanopub/7/
ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/nanopub/8/
ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/nanopub/9/
ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/derived_data_file/3
ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/raw_data_file/17
ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/raw_data_file/18
ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/raw_data_file/19
ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/raw_data_file/20
ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/raw_data_file/21
### Demonstrate of RO used for minimally preserving workflows
# Add workflow description (wfdesc)
# http://gigagalaxy.net/u/peterli/w/assembling-the-s-aureus-genome-using-soapdenovo2
ro annotate Workflows/Galaxy-Workflow-Workflow_constructed_from_history__reproduce_s.aureus_pipeline_.ga -g Galaxy-wfdesc.rdf
# Annotate selelcted input data
ro link Workflows/Galaxy-Workflow-Workflow_constructed_from_history__reproduce_s.aureus_pipeline_.ga roterms:inputSelected http://w3id.org/isa/soapdenovo2/raw_data_file/17
ro link Workflows/Galaxy-Workflow-Workflow_constructed_from_history__reproduce_s.aureus_pipeline_.ga roterms:inputSelected http://w3id.org/isa/soapdenovo2/raw_data_file/18
ro link Workflows/Galaxy-Workflow-Workflow_constructed_from_history__reproduce_s.aureus_pipeline_.ga roterms:inputSelected http://w3id.org/isa/soapdenovo2/raw_data_file/19
ro link Workflows/Galaxy-Workflow-Workflow_constructed_from_history__reproduce_s.aureus_pipeline_.ga roterms:inputSelected http://w3id.org/isa/soapdenovo2/raw_data_file/20
ro link Workflows/Galaxy-Workflow-Workflow_constructed_from_history__reproduce_s.aureus_pipeline_.ga roterms:inputSelected http://w3id.org/isa/soapdenovo2/raw_data_file/21
# Annotate output data
ro annotate Outputs/gage.out.Tabular -g output.rdf
# Show all annotations
ro annotations
# publish an RO
#ro push -d . -r "http://sandbox.wf4ever-project.org/rodl/ROs/" -t "73975122-9503-4000-ba52-d2c2d2bfccbb"
# End.