Using Job DSL Plugin with Active Choices Plugin
The Active Choices plugin can be used to increase the reactiveness of your parameters. Using the plugin, you are able to better plan how your parameters will...
Posts by Tag
- jenkins 10
- workflow 7
- Jenkins 7
- analysis 7
- bioinformatics 7
- news 6
- plugins 5
- data-sciences 5
- announce 4
- update-center 3
- metadata 3
- life-sciences 3
- reporting 3
- pbs 2
- java 2
- api 2
- drmaa 2
- jenkins" 2
- project-meeting 2
- uno-choice-plugin 1
- dnadigest 1
- hackday 1
- pipelines 1
- R 1
- R Plug-in 1
- tutorial 1
- biojs 1
- imaging 1
- Active-Choices 1
- CloudBees 1
- Kohsuke Kawaguchi 1
- Jesse Glick 1
- post-mortem 1
jenkins
What happens when you make a Java member variable transient in a Jenkins plug-in
This blog post is a post mortem. Even though it is not exactly about an outage in a system, as it is common to be announced in post mortems, it is still a bi...
Java DRMAA API — part 2
This is the first part of a series of posts about a Java API for PBS servers, compliant with the DRMAA spec.
Java DRMAA API — part 1
This is the first part of a series of posts about a Java API for PBS servers, compliant with the DRMAA spec. PBS is a type of batch server, or distributed r...
Experiences from JUC 2014 Boston
On June 18th, I attended my first ever Jenkins User Conference in Boston, USA.
Playing with BioJS
In the post entitled The Secret of Building a scientific community, Manuel Corpas describe his experiences coordinating the BiosJS project. It is a great w...
rOpenSci in Jenkins
rOpenSci is an Open Data project. It has many R packages that access several data repositories. In this post we will demonstrate how to use rOpenSci taxize p...
Uno-Choice: Our first user contributed plug-in
Uno-Choice has been released and is our first user contributed plug-in. This plug-in was proposed by Ioannis Moutsatsos, and has been described as a “propos...
More plug-ins released
In the past days two more plug-ins were released to our update center. The plug-ins are CLUMPP plug-in and Structure Harvester plug-in. Before that the fir...
Announcing the BioUno Update Center for Jenkins plug-ins
We are happy to announce that the Jenkins plug-ins developed in the BioUno project will be now available online to all Jenkins instances through the plug-in...
workflow
Advanced Cross-Project Linking of Jenkins Artifacts
Introduction In Documenting Data with Metadata we discussed how Jenkins lacks a built-in framework for relating arbitrary Jenkins projects, builds, and arti...
Jenkins: Documenting Data with Metadata
Data without associated annotation and metadata (documentation describing the data) is of little lasting value 1. It is imperative that each dataset used for...
Is it Wow or Just about Time?
We all know and love Jenkins despite some of its historical quirks. The community is now on a march to introduce some new concepts and a more modern UI that ...
Meeting the creator of my favorite automation server
What do you do when you see a tweet announcing that Kohsuke Kawaguchi (the creator of Jenkins CI) is looking to meet in your area with ‘real-world developers...
Creating a Jenkins Data Science Platform
Having worked with Jenkins-CI in the life sciences context for the last few years, I am finding that Jenkins satisfies key requirements of a robust framework...
Consistent Reports for Data Analysis
When you use Jenkins for analytics it is important to deliver consistent analysis reports from each build. There are a few different ways that you can create...
Experiences from JUC 2014 Boston
On June 18th, I attended my first ever Jenkins User Conference in Boston, USA.
Jenkins
Advanced Cross-Project Linking of Jenkins Artifacts
Introduction In Documenting Data with Metadata we discussed how Jenkins lacks a built-in framework for relating arbitrary Jenkins projects, builds, and arti...
Jenkins: Documenting Data with Metadata
Data without associated annotation and metadata (documentation describing the data) is of little lasting value 1. It is imperative that each dataset used for...
Is it Wow or Just about Time?
We all know and love Jenkins despite some of its historical quirks. The community is now on a march to introduce some new concepts and a more modern UI that ...
Meeting the creator of my favorite automation server
What do you do when you see a tweet announcing that Kohsuke Kawaguchi (the creator of Jenkins CI) is looking to meet in your area with ‘real-world developers...
Creating a Jenkins Data Science Platform
Having worked with Jenkins-CI in the life sciences context for the last few years, I am finding that Jenkins satisfies key requirements of a robust framework...
From Uno-Choice to Active Choices
More than a year ago I approached Bruno via a series of posts on the BioUno developer’s forum and discussed my frustration with the available Jenkins user in...
Consistent Reports for Data Analysis
When you use Jenkins for analytics it is important to deliver consistent analysis reports from each build. There are a few different ways that you can create...
analysis
Advanced Cross-Project Linking of Jenkins Artifacts
Introduction In Documenting Data with Metadata we discussed how Jenkins lacks a built-in framework for relating arbitrary Jenkins projects, builds, and arti...
Jenkins: Documenting Data with Metadata
Data without associated annotation and metadata (documentation describing the data) is of little lasting value 1. It is imperative that each dataset used for...
Is it Wow or Just about Time?
We all know and love Jenkins despite some of its historical quirks. The community is now on a march to introduce some new concepts and a more modern UI that ...
Meeting the creator of my favorite automation server
What do you do when you see a tweet announcing that Kohsuke Kawaguchi (the creator of Jenkins CI) is looking to meet in your area with ‘real-world developers...
Creating a Jenkins Data Science Platform
Having worked with Jenkins-CI in the life sciences context for the last few years, I am finding that Jenkins satisfies key requirements of a robust framework...
From Uno-Choice to Active Choices
More than a year ago I approached Bruno via a series of posts on the BioUno developer’s forum and discussed my frustration with the available Jenkins user in...
Consistent Reports for Data Analysis
When you use Jenkins for analytics it is important to deliver consistent analysis reports from each build. There are a few different ways that you can create...
bioinformatics
Advanced Cross-Project Linking of Jenkins Artifacts
Introduction In Documenting Data with Metadata we discussed how Jenkins lacks a built-in framework for relating arbitrary Jenkins projects, builds, and arti...
Jenkins: Documenting Data with Metadata
Data without associated annotation and metadata (documentation describing the data) is of little lasting value 1. It is imperative that each dataset used for...
Is it Wow or Just about Time?
We all know and love Jenkins despite some of its historical quirks. The community is now on a march to introduce some new concepts and a more modern UI that ...
Meeting the creator of my favorite automation server
What do you do when you see a tweet announcing that Kohsuke Kawaguchi (the creator of Jenkins CI) is looking to meet in your area with ‘real-world developers...
Creating a Jenkins Data Science Platform
Having worked with Jenkins-CI in the life sciences context for the last few years, I am finding that Jenkins satisfies key requirements of a robust framework...
From Uno-Choice to Active Choices
More than a year ago I approached Bruno via a series of posts on the BioUno developer’s forum and discussed my frustration with the available Jenkins user in...
Consistent Reports for Data Analysis
When you use Jenkins for analytics it is important to deliver consistent analysis reports from each build. There are a few different ways that you can create...
news
USP 2nd High Performance Computing Workshop and Bioinformatics pipelines
I have just returned from Universidade de Sao Paulo, where I attended the [2º High Performance Computing Workshop](http://2whpc.lcca.usp.br/). Unfortun...
DNADigest Hackday and Metadata
DNADigest held a free Hackday this past Saturday, April 5th, in London. Luckily they also live transmitted the event via Internet, and it was definitely wor...
Uno-Choice: Our first user contributed plug-in
Uno-Choice has been released and is our first user contributed plug-in. This plug-in was proposed by Ioannis Moutsatsos, and has been described as a “propos...
More plug-ins released
In the past days two more plug-ins were released to our update center. The plug-ins are CLUMPP plug-in and Structure Harvester plug-in. Before that the fir...
Announcing the BioUno Update Center for Jenkins plug-ins
We are happy to announce that the Jenkins plug-ins developed in the BioUno project will be now available online to all Jenkins instances through the plug-in...
The BioUno blog is live
We are migrating our old web site to GitHub pages. We expect that it will make typos, new docs and suggestions easier to get fixed, merged and released. Fee...
plugins
Changing the type of an attribute serialized by XStream in Jenkins Plug-ins
This post was written while fixing JENKINS-23772 for the Image Gallery Plug-in. This plug-in can be used to create image galleries for artifacts found in the...
Using Jenkins Credentials Plug-in to create the BioUno figshare Plug-in
figshare is a platform where users can upload and share images, graphs, presentations and other documents. These artifacts can be generated using different t...
Uno-Choice: Our first user contributed plug-in
Uno-Choice has been released and is our first user contributed plug-in. This plug-in was proposed by Ioannis Moutsatsos, and has been described as a “propos...
More plug-ins released
In the past days two more plug-ins were released to our update center. The plug-ins are CLUMPP plug-in and Structure Harvester plug-in. Before that the fir...
Announcing the BioUno Update Center for Jenkins plug-ins
We are happy to announce that the Jenkins plug-ins developed in the BioUno project will be now available online to all Jenkins instances through the plug-in...
data-sciences
Advanced Cross-Project Linking of Jenkins Artifacts
Introduction In Documenting Data with Metadata we discussed how Jenkins lacks a built-in framework for relating arbitrary Jenkins projects, builds, and arti...
Jenkins: Documenting Data with Metadata
Data without associated annotation and metadata (documentation describing the data) is of little lasting value 1. It is imperative that each dataset used for...
Is it Wow or Just about Time?
We all know and love Jenkins despite some of its historical quirks. The community is now on a march to introduce some new concepts and a more modern UI that ...
Meeting the creator of my favorite automation server
What do you do when you see a tweet announcing that Kohsuke Kawaguchi (the creator of Jenkins CI) is looking to meet in your area with ‘real-world developers...
Creating a Jenkins Data Science Platform
Having worked with Jenkins-CI in the life sciences context for the last few years, I am finding that Jenkins satisfies key requirements of a robust framework...
announce
Uno-Choice: Our first user contributed plug-in
Uno-Choice has been released and is our first user contributed plug-in. This plug-in was proposed by Ioannis Moutsatsos, and has been described as a “propos...
More plug-ins released
In the past days two more plug-ins were released to our update center. The plug-ins are CLUMPP plug-in and Structure Harvester plug-in. Before that the fir...
Announcing the BioUno Update Center for Jenkins plug-ins
We are happy to announce that the Jenkins plug-ins developed in the BioUno project will be now available online to all Jenkins instances through the plug-in...
The BioUno blog is live
We are migrating our old web site to GitHub pages. We expect that it will make typos, new docs and suggestions easier to get fixed, merged and released. Fee...
update-center
Uno-Choice: Our first user contributed plug-in
Uno-Choice has been released and is our first user contributed plug-in. This plug-in was proposed by Ioannis Moutsatsos, and has been described as a “propos...
More plug-ins released
In the past days two more plug-ins were released to our update center. The plug-ins are CLUMPP plug-in and Structure Harvester plug-in. Before that the fir...
Announcing the BioUno Update Center for Jenkins plug-ins
We are happy to announce that the Jenkins plug-ins developed in the BioUno project will be now available online to all Jenkins instances through the plug-in...
metadata
Advanced Cross-Project Linking of Jenkins Artifacts
Introduction In Documenting Data with Metadata we discussed how Jenkins lacks a built-in framework for relating arbitrary Jenkins projects, builds, and arti...
Jenkins: Documenting Data with Metadata
Data without associated annotation and metadata (documentation describing the data) is of little lasting value 1. It is imperative that each dataset used for...
DNADigest Hackday and Metadata
DNADigest held a free Hackday this past Saturday, April 5th, in London. Luckily they also live transmitted the event via Internet, and it was definitely wor...
life-sciences
From Uno-Choice to Active Choices
More than a year ago I approached Bruno via a series of posts on the BioUno developer’s forum and discussed my frustration with the available Jenkins user in...
Consistent Reports for Data Analysis
When you use Jenkins for analytics it is important to deliver consistent analysis reports from each build. There are a few different ways that you can create...
Experiences from JUC 2014 Boston
On June 18th, I attended my first ever Jenkins User Conference in Boston, USA.
reporting
Is it Wow or Just about Time?
We all know and love Jenkins despite some of its historical quirks. The community is now on a march to introduce some new concepts and a more modern UI that ...
Creating a Jenkins Data Science Platform
Having worked with Jenkins-CI in the life sciences context for the last few years, I am finding that Jenkins satisfies key requirements of a robust framework...
Consistent Reports for Data Analysis
When you use Jenkins for analytics it is important to deliver consistent analysis reports from each build. There are a few different ways that you can create...
pbs
Java DRMAA API — part 2
This is the first part of a series of posts about a Java API for PBS servers, compliant with the DRMAA spec.
Java DRMAA API — part 1
This is the first part of a series of posts about a Java API for PBS servers, compliant with the DRMAA spec. PBS is a type of batch server, or distributed r...
java
Java DRMAA API — part 2
This is the first part of a series of posts about a Java API for PBS servers, compliant with the DRMAA spec.
Java DRMAA API — part 1
This is the first part of a series of posts about a Java API for PBS servers, compliant with the DRMAA spec. PBS is a type of batch server, or distributed r...
api
Java DRMAA API — part 2
This is the first part of a series of posts about a Java API for PBS servers, compliant with the DRMAA spec.
Java DRMAA API — part 1
This is the first part of a series of posts about a Java API for PBS servers, compliant with the DRMAA spec. PBS is a type of batch server, or distributed r...
drmaa
Java DRMAA API — part 2
This is the first part of a series of posts about a Java API for PBS servers, compliant with the DRMAA spec.
Java DRMAA API — part 1
This is the first part of a series of posts about a Java API for PBS servers, compliant with the DRMAA spec. PBS is a type of batch server, or distributed r...
jenkins"
Changing the type of an attribute serialized by XStream in Jenkins Plug-ins
This post was written while fixing JENKINS-23772 for the Image Gallery Plug-in. This plug-in can be used to create image galleries for artifacts found in the...
Using Jenkins Credentials Plug-in to create the BioUno figshare Plug-in
figshare is a platform where users can upload and share images, graphs, presentations and other documents. These artifacts can be generated using different t...
project-meeting
BioUno meeting 2016-11-18
Participants: Bruno P. Kinoshita and Ioannis K. Moutsatsos. 2016-11-18 08:00 PM UTC using Google Hangouts.
BioUno meeting 2016-07-27
Participants: Bruno P. Kinoshita and Ioannis K. Moutsatsos. 2016-07-27 08:00 PM UTC using Google Hangouts.
uno-choice-plugin
Uno-Choice: Our first user contributed plug-in
Uno-Choice has been released and is our first user contributed plug-in. This plug-in was proposed by Ioannis Moutsatsos, and has been described as a “propos...
dnadigest
DNADigest Hackday and Metadata
DNADigest held a free Hackday this past Saturday, April 5th, in London. Luckily they also live transmitted the event via Internet, and it was definitely wor...
hackday
DNADigest Hackday and Metadata
DNADigest held a free Hackday this past Saturday, April 5th, in London. Luckily they also live transmitted the event via Internet, and it was definitely wor...
pipelines
USP 2nd High Performance Computing Workshop and Bioinformatics pipelines
I have just returned from Universidade de Sao Paulo, where I attended the [2º High Performance Computing Workshop](http://2whpc.lcca.usp.br/). Unfortun...
R
rOpenSci in Jenkins
rOpenSci is an Open Data project. It has many R packages that access several data repositories. In this post we will demonstrate how to use rOpenSci taxize p...
R Plug-in
rOpenSci in Jenkins
rOpenSci is an Open Data project. It has many R packages that access several data repositories. In this post we will demonstrate how to use rOpenSci taxize p...
tutorial
rOpenSci in Jenkins
rOpenSci is an Open Data project. It has many R packages that access several data repositories. In this post we will demonstrate how to use rOpenSci taxize p...
biojs
Playing with BioJS
In the post entitled The Secret of Building a scientific community, Manuel Corpas describe his experiences coordinating the BiosJS project. It is a great w...
imaging
Experiences from JUC 2014 Boston
On June 18th, I attended my first ever Jenkins User Conference in Boston, USA.
Active-Choices
From Uno-Choice to Active Choices
More than a year ago I approached Bruno via a series of posts on the BioUno developer’s forum and discussed my frustration with the available Jenkins user in...
CloudBees
Meeting the creator of my favorite automation server
What do you do when you see a tweet announcing that Kohsuke Kawaguchi (the creator of Jenkins CI) is looking to meet in your area with ‘real-world developers...
Kohsuke Kawaguchi
Meeting the creator of my favorite automation server
What do you do when you see a tweet announcing that Kohsuke Kawaguchi (the creator of Jenkins CI) is looking to meet in your area with ‘real-world developers...
Jesse Glick
Meeting the creator of my favorite automation server
What do you do when you see a tweet announcing that Kohsuke Kawaguchi (the creator of Jenkins CI) is looking to meet in your area with ‘real-world developers...
post-mortem
What happens when you make a Java member variable transient in a Jenkins plug-in
This blog post is a post mortem. Even though it is not exactly about an outage in a system, as it is common to be announced in post mortems, it is still a bi...