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iPlant Tool Integration Process

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2 Virtual Iron 2 Big Iron Commod ity Iron Algorith ms: Big Small Data: Big Small Plant Biologists Community Computational Biologists iPlant Cyberinfrastructure High-Level View of iPlant CI

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What we need How to download the tool or source code, including installation and usage instructions. The required version of the program. A sample dataset and the expected results to be output. The set of parameters and command line switches that match the expected execution of the tool. A brief text description of the tool, written for someone who has not used the tool before. This should include links to literature for further reading.

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5 A few things to keep in mind iPlants resources are limited iPlant cannot generate new data iPlant needs collaborators with expertise Complex data integration and interactive visualization are big problems 5 Biology and Computer Science have technical jargon: Clear communication and patience are essential!

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JSON

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{ "name": "iPlant Collaborative", "address": { "street": "E Helen St", "number": 1657, "city": "Tucson", "state": "AZ", "ZIP": 85721 }, "contacts": [ { "first name": "Naim", "last name": "Matasci", "function": "Engagement Team Analyst", "telephone": { "prefix": 520, "number": "626-3756" }, "email": [ "nmatasci@iplantcollborative.org", "matasci@email.arizona.edu" ] }, { "first name": "Sonya", "last name": "Lowry", "function": "Director of Cyberinfrastructure Development ", "telephone": { "prefix": "520", "number": "626-9104" }, "email": "sonya@iplantcollaborative.org" } ] }

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Tool metadata What is being integrated?

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What? Name: Tool name Description: What the tool does Type: "executable" (more will come) [location]: Where the executable reside (we'll tell you that) Attribution: Who wrote it Version: Which version (we want to get the right thing)

Slide 12 cat d infile >outfile"> command [options] infiles outfiles { "name": "cat", "description": "Reads the contents of a file and writes it to standard output", "type": "executa">

> command [options] infiles outfiles { "name": "cat", "description": "Reads the contents of a file and writes it to standard output", "type": "executable", "location": "/bin/cat", "attribution": "A really smart UNIX guru like Rob Pike wrote the original version. A cat utility appeared in Version 1 AT&T UNIX. Dennis Ritchie designed and wrote the first man page.", "version": "7.4.1", } > cat d infile >outfile

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Tool Interface Metadata How is it integrated?

Slide 14 command [options] infiles outfiles Outfi"> command [options] infiles outfiles Outfiles"> command [options] infiles outfiles Outfi" title="{ "id":"", "name": "", "type": "", "input":[... ], "groups": [... ], "output":[... ] } Info Infiles Options > command [options] infiles outfiles Outfi">

{ "id":"", "name": "", "type": "", "input":[... ], "groups": [... ], "output":[... ] } Info Infiles Options > command [options] infiles outfiles Outfiles

Slide 15 cat b filename.txt >out.txt From the metadata description"> cat b filename.txt >out.txt From the metadata description"> cat b filename.txt >out.txt From the metadata description" title="{ "id":"", "name": "Linux cat", "type": "cat", "input":[], "groups":[] "output":[] } >cat b filename.txt >out.txt From the metadata description">

{ "id":"", "name": "Linux cat", "type": "cat", "input":[], "groups":[] "output":[] } >cat b filename.txt >out.txt From the metadata description

Slide 16 cat b fi"> cat b filename.txt >out.txt"> cat b fi" title="{ "input":[ { "id":"catin", "name":"File to read:", "type":"File", "multiplicity":"single", "order":2 }, ], "groups": [], "output":[] } >cat b fi">

{ "input":[ { "id":"catin", "name":"File to read:", "type":"File", "multiplicity":"single", "order":2 }, ], "groups": [], "output":[] } >cat b filename.txt >out.txt

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{ "groups": [ { "name": "Options", "id": "", "type": "step", "properties": [ { "id":"bflag", "name":" -b ", "type":"Flag", "label":"Show line numbers", "visible":true, "value": true, "validator":{ "name":"", "required":true }, "order":1 } ] } ], Grouping of options, panels. Parameters, options to set

Slide 18 " } ] }"> " } ] }"> " } ] }" title=">cat b filename.txt >out.txt {... "output":[ { "id":"catout", "name":"", "type":"file", "multiplicity":"single", "order":3 "switch":" > " } ] }">

>cat b filename.txt >out.txt {... "output":[ { "id":"catout", "name":"", "type":"file", "multiplicity":"single", "order":3 "switch":" > " } ] }

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For R? Not much different

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>Rscript --env script.R [options] Rscript --env script.R [options] [options]

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Single site Tool Metadata { "location" : "/usr/bin/Rscript", "name" : "singleSite", "type" : "executable", "version" : 1.0, "description" : "Single Site analysis for breeding platform", "attribution" : "Graham McLaren (g.mclaren@cgiar.org)" }

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singleSite.R data_1cat b filename.txt | grep cat -b grep Filename.txt">

>cat b filename.txt | grep cat -b grep Filename.txt

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{ "analysis_id":"", "analysis_name":"File Read and Display", "type":"Concatenate and print a file", "description":"Reads a file and prints to standard output", "steps":[ { "name":"cat", "description":"Reads a file and prints to standard output", "template_id":"", "config":{ } }, { "name":"grep_search", "description":"Searches within a file for supplied text", "template_id":"", "config":{ } }, ]

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"mapping":[ { "source_step":"cat", "target_step":"grep_search", "map":{ "catout":"grepin" } }, ]

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Complete material & tutorials at: http://www.iplantcollaborative.org https://pods.iplantcollaborative.org/wiki/display/docs/Analysis+Authoring+Tutorial https://pods.iplantcollaborative.org/wiki/display/docs/Tool+Integration+Tutorial