jenkins-ci: automating lab processes

Department of Bioinformatics - BiGCaT 1

Jenkins-CI

automating lab processes

Science Cafe

Maastricht, 2 October 2014

Department of Bioinformatics - BiGCaT 2

CI := Continuous Integration

• Continuous– Automation: while you write grants or

teach– Reactive: when people commit changes

• Integration– Compile starts when something else

(successfully) compiled– Plugins...

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What is Jenkins-CI?

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Just software? No.

• “Jenkins High throughput Screening”

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Just software? No.

• “Jenkins High throughput Screening”

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Jenkins 4 BiGCaT

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BridgeDb: alternative builds

• Ant + Maven• Branches• R package

– builds when ...

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PathVisio plugins

• Recompile for every new PathVisio build

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What if the build fails?

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Unit / regression / ... testing?

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Computer-Assisted WikiPathways Curation

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Detect common problems

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What problems?

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Example “error message”

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Source code

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Jenkins 4 eNanoMapper

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Ontology integration & testing

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User Authentication

• BiGCaT– unimaas!

• Jenkins– OpenTox LDAP

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Big thanks Nuno!

PS. this presentation show what Jenkins can do. All things running as jobs are work from others. Make sure to follow

the links to the GitHub projects for many of these jobs to see the heroes of that

project!