sushi – an exquisite recipe for ngs data analysis hubert rehrauer & masaomi hatakeyama...
TRANSCRIPT
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Sushi – An exquisite recipe for NGS data analysis
Hubert Rehrauer & Masaomi Hatakeyama
Supporting User for SHell-script Integration
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What is your data analysis wishlist?
We had in mind:• analyze by clicking• scriptable• manage my meta-information• document all analysis steps• organize my work
• I can add analysis applications• connects to my compute resources• keep everything in files on my disk• no painful file formats
The bioinformatician stays in the driver seat
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The Sushi idea (I)
Start with a bunch of raw data files on your disk:
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The Sushi idea (II)
Add the magic seasoning: Meta information
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Meta-information turns mere data files into a data set
One r
ow
per
sam
ple
associated files
everything else noteworthy about the files and the samples
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Sushi offers a choice of analysis apps for your data set
The meta-information columns drive the available applications
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Sushi lets you control all parameters
as selectors
or
as free text
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The processing jobs generate the data files …
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Sushi adds all ingredients to make them a new, documented data set …
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… and Sushi let’s you move to the next analysis
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The Sushi Data Analysis Process
• Step 1– Generate Job script(s)
• Step 2– Submit the Job script(s)
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Sushi Modules
1. Sushi UI– Ruby on Rails– GUI
2. Sushi Application– Single Ruby file– CLI
3. Workflow Manager– Ruby gem library– Job Control
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Sushi Components at FGCZ
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Sushi Rank
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Why choose Sushi?
• It has never been easier to import meta-information• It has never been easier to add new data analysis
applications• Sushi does not impose constraints on your data analysis
Your applications define the semantics• You never have to export your data again
it’s already exported!• You never have to document your analysis again
the result is fully self-contained and documented by the time the analysis is done• Sushi keeps your work organized even if you work on 10
different projects with thousands of samples
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Acknowledgements
• FGCZ Genome Informatics Team• Giancarlo Russo• Lennart Opitz• Weihong Qi• Slavica Dimitrieva
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Sushi Takeaways
•S•U•S•H•I
•SUSHI•Super Easy Pipeline System
•Ultra Fast Development
•Surprisingly Flexible Ruby code
•Highly Independent Modules
•Intermediary between biologist and informatician
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Sushi Demo 10 minutes
1.Installation 1 min
2.Data import/Job submission 2 mins
3.New application import 3 mins
4.Case Study 4 mins–RNAseq DEG analysis
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Demo Environment
• Mac OS X 10.9.4• Ruby 1.9.3• Ruby on Rails 3.2.9
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Installation
1. Downloading Ruby on Rails package– http://fgcz-sushi.uzh.ch/sushi_20140908.tgz
2. Install libraries– bundle install
3. Setup DB– bundle exec rake db:migrate
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Documents
fgcz-sushi.uzh.ch
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Download
fgcz-sushi.uzh.ch/download.html
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InstallationDownload, Extraction, Library installation, DB setup
$ wget http://fgcz-sushi.uzh.ch/sushi_20140908.tgz $ tar zxvf sushi_20140908.tgz $ cd sushi $ bundle install $ bundle exec rake db:migrate
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Sushi run, workflow_manager run
$ rails server
$ workflow_manager
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Sushi Access
localhost:3000
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Data import / Job submission
• Prepare your data set• Import dataset.tsv• Check samples• Select an application–WordCountApp
• Set parameters• Submit a job• Check job status• Check job script/log– public/projects
• Check result
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DataSet Import
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DataSet Import
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New Application Import
fgcz-sushi.uzh.ch/download.html
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New Application Import
$ wget http://fgcz-sushi.uzh.ch/fgcz_sushi_apps.tgz$ tar xvf fgcz_sushi_apps.tgz$ cp fgcz_sushi_apps/FastqcApp.rb sushi/lib/ $ cp -r fgcz_sushi_apps/R_scripts sushi/lib/
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A Case Study –RNAseq DEG analysis-
• RNAseq Analysis– Quality Control– FastQC
–Mapping– STAR
– Counting– HTSeq
– Differential Gene Expression– EdgeR
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Summary
• Shell script auto-generating• Application Framework• Support all languages• Help bio-logist/-informatician• Implemented in Ruby• Meta-Information DataSet• Interface: GUI / CLI
• S• A• S• H• I• M• I
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Thank you for your attention!!
http://fgcz-sushi.uzh.ch
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Data import / Job submission
• Prepare your data set• Import dataset.tsv• Check samples• Select an application–WordCountApp
• Set parameters• Submit a job• Check job status• Check job script/log– public/projects
• Check result
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DataSet Import
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DataSet Import
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DataSet Import
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DataSet
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DataSet
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Sushi Application Run
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Parameter Setting
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Job Submission
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Job Status
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New DataSet
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Log, Job Script
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Log, Job Script
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Job Script
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Job Script
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New Application Import
fgcz-sushi.uzh.ch/download.html
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New Application Import
$ wget http://fgcz-sushi.uzh.ch/fgcz_sushi_apps.tar$ tar xvf fgcz_sushi_apps.tar$ cp fgcz_sushi_apps/FastqcApp.rb sushi/lib/ $ cp -r fgcz_sushi_apps/R_scripts sushi/lib/
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New Application Import
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FastQC result
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A Case Study –RNAseq DEG analysis-
• RNAseq Analysis– Quality Control– FastQC
–Mapping– STAR
– Counting– HTSeq
– Differential Gene Expression– EdgeR
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A Case Study
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Summary
• Shell script auto-generating• Application Framework• Support all languages• Help bio-logist/-informatician• Implemented on Ruby• Meta-Information DataSet• Interface: GUI / CLI
• S• A• S• H• I• M• I
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Thank you for your attention!!
http://fgcz-sushi.uzh.ch
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Appendix
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Sushi Run Style
• GUI
• CLI
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Application Mode
1. SAMPLE mode– Job per Sample, e.g. Tophat
2. DATASET mode– Job per DataSet, e.g. FastQC
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Import New Application
• 2 ways: prepare 1. Shell script 2. Ruby script
• Save it in Sushi repository– lib directory– No reboot
• Test on CLI– $ sushi_fabric --class WordCountApp --dataset_id 1 –run
• Test on GUI
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How to add a new application
1. Inherit SushiApp class –Write Ruby code– Template Method Design Pattern– Possible to tune-up details
2. Delegate to SushiWrap class–Write Shell script– Ruby Metaprogramming– Quick import
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Template Method Pattern
• Write Ruby code directly
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Meta-programming
• Ruby code auto generation– from shell script code
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A Sushi App – WordCountApp.rb
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A Sushi App – WordCount.sh
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The R Sushi Apps – FastqcApp.rb
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Structure of a Job Script
Generated by Sushi
Generated by Sushi
Generated by App
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Sushi gem
• https://rubygems.org/gems/sushi_fabric