Jenkins Plug-ins
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 an 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.
| Computer Management | |||
|---|---|---|---|
| PBS Plug-in | PBS (Portable Batch System) is the name of computer software that performs job scheduling. Its primary task is to allocate computational tasks, i.e., batch jobs, among the available computing resources. It is often used in conjunction with UNIX cluster environments. | Torque PBS - http://www.adaptivecomputing.com/products/open-source/torque/ | pbs.hpi |
| Phylogenetics | |||
| MrBayes Plug-in | MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters. | MrBayes - http://mrbayes.sourceforge.net/ | mrbayes.hpi |
| FigTree Plug-in | FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures | FigTree - http://tree.bio.ed.ac.uk/software/figtree/ | figtree.hpi |
| Genetic Analysis | |||
| Structure Plug-in | The program structure is a free software package for using multi-locus genotype data to investigate population structure. | Structure - http://pritch.bsd.uchicago.edu/software.html | structure.hpi |
Other recommended Jenkins plug-ins
Jenkins has a lot of other useful plug-ins that you should consider using when configuring your jobs.
| 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. |