jenkins-ci: automating lab processes
Post on 18-Dec-2014
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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...
Department of Bioinformatics - BiGCaT 3
What is Jenkins-CI?
Department of Bioinformatics - BiGCaT 4
Just software? No.
• “Jenkins High throughput Screening”
Department of Bioinformatics - BiGCaT 5
Just software? No.
• “Jenkins High throughput Screening”
Department of Bioinformatics - BiGCaT 6
Department of Bioinformatics - BiGCaT 7
Jenkins 4 BiGCaT
Department of Bioinformatics - BiGCaT 8
BridgeDb: alternative builds
• Ant + Maven• Branches• R package
– builds when ...
Department of Bioinformatics - BiGCaT 9
PathVisio plugins
• Recompile for every new PathVisio build
Department of Bioinformatics - BiGCaT 10
What if the build fails?
Department of Bioinformatics - BiGCaT 11
Unit / regression / ... testing?
Department of Bioinformatics - BiGCaT 12
Computer-Assisted WikiPathways Curation
Department of Bioinformatics - BiGCaT 13
Detect common problems
Department of Bioinformatics - BiGCaT 14
What problems?
Department of Bioinformatics - BiGCaT 15
Example “error message”
Department of Bioinformatics - BiGCaT 16
Source code
Department of Bioinformatics - BiGCaT 17
Jenkins 4 eNanoMapper
Department of Bioinformatics - BiGCaT 18
Ontology integration & testing
Department of Bioinformatics - BiGCaT 19
Department of Bioinformatics - BiGCaT 20
User Authentication
• BiGCaT– unimaas!
• Jenkins– OpenTox LDAP
Department of Bioinformatics - BiGCaT 21
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!
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