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Continuous Integration tools and techniques applied in Bioinformatics

Using Jenkins gives us not only the possibility to use its job scheduling, monitoring and triggering, and notifications. We can also extend Jenkins with plug-ins. There is a Jenkins update site for BioUno which stores all bio-plugins, like MrBayes and FigTree.

You can install any plug-in automatically using the Web user interface or by running a command in your shell.

Grid computing
PBS Plug-in This plug-ins lets you use Jenkins to control a Torque PBS cluster.
MrBayes Plug-in Integrates MrBayes and Jenkins.
FigTree Plug-in Integrates FigTree and Jenkins.
Genetic Analysis
Structure Plug-in Integrates Structure and Jenkins.
Structure Harvester Plug-in Integrates Structure Harvester and Jenkins.
CLUMPP Plug-in Integrates CLUMPP and Jenkins.
Distruct Plug-in Integrates Distruct and Jenkins.
Uno-Choice Plug-in A proposal for a new Jenkins UI plugin for selecting one or multiple parameters. Attempting to fill the gaps left by current plugin options.
Image Gallery Plug-in This plug-in reads a job workspace and collects images to produce an image gallery using colorbox lightbox Javascript library.
R Plug-in A simple plug-in to invoke R interpreter and execute an R script.

Jenkins already has several plug-ins that you can find useful for your lab. We have listed a few plug-ins below with a brief description.

Plug-in name Description
Build Pipeline Plug-in For managing your build pipelines.
JobConfigHistory Plug-in To keep a history of your job configuration changes.
Build Timeout Plug-in To limit the time of your jobs.
Backup Plugin For creating back ups for your Jenkins instance and jobs.
E-mail-ext Plug-in Lets you easily configure e-mail notifications for different actions in Jenkins.
Git Plug-in For storing biology data in GitHub.
Timestamper Plug-in Adds timestamps to the Console Output.