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Open Source Software for Scientific Application

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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. More information about it in the PBS Plug-in GitHub Wiki
FigTree Plug-in Integrates FigTree and Jenkins.
MrBayes Plug-in Integrates MrBayes and Jenkins.
Genetic Analysis
CLUMPP Plug-in Integrates CLUMPP and Jenkins.
Distruct Plug-in Integrates Distruct and Jenkins.
Structure Plug-in Integrates Structure and Jenkins.
Structure Harvester Plug-in Integrates Structure Harvester and Jenkins.
Chemical Structures
Jmol Plug-in Renders Jmol molecules in the build page, using Jmol Javascript library
Active Choices Plugin A Jenkins UI plugin for selecting one or multiple options for a job parameter. The UI control can be rendered in a variety of ways including dynamic HTML
Image Gallery Plug-in This plug-in reads a job workspace and collects images to produce an image gallery using colorbox lightbox Javascript library.
figshare Plug-in This plug-in integrates figshare and Jenkins, using figshare API v1 with OAuth 1.0 and the Credentials Plug-in.
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.
Summary Display Plugin Generates dynamic, rich summary reports on build pages. The reports are written in a consistent XML format.
Timestamper Plug-in Adds timestamps to the Console Output.