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Jenkins and Bioinformatics, catch us at BOSC 2012

[ Editor's Note: The following is a post from Jenkins CIA member Bruno P. Kinoshita ]

Jenkins will be represented at this years Bioinformatics Open Source Conference (BOSC 2012) on July 13-14th in Long Beach, California. I will be talking about Jenkins during my talk about BioUno.

BOSC 2012 will be held just before ISMB 2012, while registration is through ISMB you don't have to register for ISMB in order to register for BOSC.

I will be at the event with some Jenkins stickers and available to answer questions you might have about BioUno and Jenkins!

About BioUno

BioUno is a project that uses Jenkins as basis for building biology workflows. BioUno provides an alternative update center with custom plug-ins for bioinformatics tools like MrBayes, Structure, Figtree, Beast, among others.

While the actual task of analysing or displaying data is handled by specific tools, that are wrapped by plug-ins, Jenkins is responsible for user control, web interface, notifications, distributed execution, job schedule and management, as well as other important low level tasks.

BioUno is similar to BioHPC, Galaxy and Taverna, in that all these tools enable creating and managing pipelines using different bioinformatics tools.

However, as it is using Jenkins, BioUno has the advantage of having an Open Source community of hackers that can answer questions and provide assistance for creating new plug-ins. There is plenty documentation for extending Jenkins and troubleshooting issues, as well as plenty existing plug-ins (that can be used as reference while writing new plug-ins).

There are projects and plug-ins that enable Jenkins to use resources in clouds or turn Jenkins into a Hadoop node, for big data processing. The next steps of the project include the deployment of BioUno to a computer facility, basic infrastructure for BioUno, definition of the process for releasing plug-ins, the creation of more plug-ins and a study on how to handle large data structures, used by many bioinformatics tools.

The project is being developed by TupiLabs under MIT License, and contributions and new plug-ins are welcome.

Jenkins a besoin de vous

[Editor's Note: The following is a guest post by Jenkins contributor Baptiste Mathus. For the non-French speakers, we're looking for French speakers to help translate "Jenkins: The Definitive Guide" ]

Woui Nide You!

Si vous vous intéressez à Jenkins et que vous aimeriez pouvoir y contribuer, lisez la suite.

L'année dernière, en août, nous avons attaqué la traduction en français du Jenkins Definitive Guide, écrit en bonne partie par John Ferguson Smart. Le travail a avancé doucement, mais a avancé tout de même. A ce jour, sur la quinzaine de chapitres, trois sont traduits et relus, et presque tout le reste est en cours.

Mais je ne parle pas bien anglais...

Ce n'est pas grave. Il y a plusieurs chapitres où il faut simplement relire, et donc parler et écrire correctement le français est suffisant. Si éventuellement, vous ne comprenez pas certaines parties traduites, et qu'il faut relire l'original, vous pouvez toujours soulever la question sur la liste de diffusion du projet où on parle français.

Je ne suis pas développeur, ou je ne connais pas Git, ou les deux

Si vous voulez vous former à Git, c'est l'occasion. On se fera un plaisir de répondre à vos questions sur la liste de diffusion, même si elles sont exclusivement liées à Git, et pas (encore) à la traduction :-).

Mais si vous ne le sentez pas ou n'avez pas le temps, ce n'est pas grave. Vous devez simplement savoir éditer un fichier XML. Il y en a un pour chaque chapitre.

Super ! Par où je commence alors ?

Si vous êtes intéressé, mais que vous avez des questions, surtout n'hésitez pas à les poser.

On vous attend ! :-)

NYC Jenkins User Conference Recap

Editor's Note: The following is a write-up courtesy of Jesse Farinacci


This past week I had the pleasure of attending the Jenkins User Conference in NYC. A hundred other like-minded continuous integration enthusiasts and I packed a very posh Marriott Marquis for a full day of Jenkins excitement.


Famed Hudson and Jenkins founder Kohsuke Kawaguchi delivered the opening address to a crowded room.

I'm sure everyone knows the statistics by now, that Jenkins adoption and development continues at an unbridled pace. Pushing past all the mailing list users and posts, the JIRAs opening and closing, the Twitter followers, the five Jenkins User Conferences scheduled for this year, the unprecedented number of installations reporting anonymous usage, the native availability for nine different OSes, in pushing past all of that..

For me, the most impressive number was that on average there was about 1 plugin created every day over the past year. Let me reiterate that: 1 plugin created every day for a year. If that isn't the best testament to the versatility, extensibility, and just plain usefulness of a piece of software, then I don't know what would be!

Announced at the conference was the general availability of CloudBees BuildHive, this is a mechanism for quickly and easily obtaining access to cloud-based Jenkins. If you have projects on GitHub, you can effortlessly log in to BuildHive via GitHub OAuth, import your projects with literally a single click, and start benefiting from the powerful promise of the cloud. You'll no longer have to worry about managing infrastructure, you'll just get all that great Jenkins CI capability for your projects immediately.

Jenkins User Conference Paris Summary

The first stop of Jenkins User Conference world tour this year was Paris, where there's a considerable concentraion of Jenkins developers and users (sometiems those of us on the other side of the Atlantic call them "the French gang") The event was held a day before Devoxx France, in the hope that we attract more attendance.

I believe there are 100+ people that actually showed up, and we had a full day divided in two tracks, talking all things about Jenkins. While many are French, some of the attendees come from all over the Europe. I was able to see some familiar faces, as well as those who I've only known by their names.

I tried to get in and out of both tracks to get the sense of what's going on, so that I can report them later, and here's my notes.

Continuous Information vol.2

Because I work on Jenkins day in day out, it's easy for me to forget that most people don't pay /that/ much attention to Jenkins. If you fit that category, and if you want to stay on top of the latest happenings in Jenkins, don’t miss Volume 2 of Continuous Information, the CloudBees Newsletter for Jenkins.

This issue...

  • Features details about the 6 upcoming Jenkins User Conferences (don’t miss these)
  • Announces the new Jenkins CIA Program (join us to promote Jenkins around the globe)
  • Shows you where to find in-depth information about the latest Jenkins UI improvements and featured plugins (cool stuff)
  • Highlights the importance of Jenkins Security Advisories (install these regularly)
  • Tells you why Jenkins has blue balls instead of green ones (seriously)
  • Shows you the latest Jenkins Usage Stats (still growing super-fast)
  • … and more great stuff, including a bit of Jenkins humor (courtesy of our friends at Geek and Poke)