IPlant Tool Integration Process. 2 Virtual Iron 2 Big Iron Commod ity Iron Algorith ms: Big Small...
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- Slide 1
- iPlant Tool Integration Process
- Slide 2
- 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
- Slide 3
- 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.
- Slide 4
- Slide 5
- 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!
- Slide 6
- JSON
- Slide 7
- Slide 8
- Slide 9
- { "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" } ] }
- Slide 10
- Tool metadata What is being integrated?
- Slide 11
- 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
- Slide 13
- 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
- Slide 17
- { "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":" > " } ] }
- Slide 19
- For R? Not much different
- Slide 20
- >Rscript --env script.R [options] Rscript --env script.R
[options] [options]
- Slide 21
- 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)" }
- Slide 22
- singleSite.R data_1cat b filename.txt | grep cat -b grep
Filename.txt">
- >cat b filename.txt | grep cat -b grep Filename.txt
- Slide 36
- { "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":{ } }, ]
- Slide 37
- "mapping":[ { "source_step":"cat", "target_step":"grep_search",
"map":{ "catout":"grepin" } }, ]
- Slide 38
- 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