Posts in tutorials

How we make our vector illustrations

Jun 14, 2012 in illustration | tutorials

Hi there!

In this blog post we will show how we make our vector illustrations. The whole process of drawing, scanning and adjusting the image levels is quite simple. The level adjustment step is required only if you think that the image is not legible enough. In some cases, you may prefer just using an eraser to remove some extra lines, shadows or stains.

Creating a PBS/MPI cluster for bioinformatics – Part 2

Apr 29, 2012 in jenkins, bioinformatics | tutorials

In the previous post of this series we saw how to configure a basic network for our small cluster. Now it is time to work on the MPI stuff. Our cluster will be a Beowulf cluster. This kind of cluster is composed of commodity computers, connected via network sharing resources and programs. And in the next post, we will see how to include a batch queuing system to control the resource utilization in our cluster.

MPI is not a library. MPI is actually a standard. When you find an RESTful application, REST is only a standard, and you have different libraries that implement this standard (Jersey, JBoss Reast Easy, CodeIgniter+Rest Controllers, and so it goes). With MPI it is not different. There are different implementations of the MPI specification. We suggest you to read this tutorial that, although it was written in 2009, it uses Debian (operational system we are using in BioUno cluster) and is very well written and concise. Basically, you have to install OpenMPI, one of the existing MPI libraries. And if you followed the instructions in part 1 of this series, then you already have SSH correctly configured in your computers.

Creating a PBS/MPI cluster for bioinformatics - Part 1

Apr 17, 2012 in jenkins, bioinformatics | tutorials

This is a series of posts with the steps we are using to set up an internal cluster for bioinformatics using MPI and PBS for distributed jobs. Our goal with this series is help other nerds setting up similar environment. This cluster is not public yet, and we are using for development of BioUno. At moment we are writing code to integrate our Jenkins with MrBayes and Structure.

In this first post, we will see how to configure the network for each machine be able to see the other one, and how to configure SSH for connecting to the other nodes in the cluster. If you already know MrBayes and Structure, skip the Introduction and go to the basic network configuration topic. We assume you have a intermediary knowledge of Linux, as many instructions in this series are vague. We always reference the original tutorial that we used. This series may be edited to stay up to date or for improvements.

Configuring Jenkins Git Plug-in with BitBucket private repositories in Windows

Feb 18, 2012 in jenkins | tutorials

Tell me about writing a specific title. This is my first entry here in TupiLabs. Today I will show you how to configure Jenkins Git Plug-in, to retrieve sources from a private repository hosted at BitBucket. Phew. Ah, and all this using a Windows server.

TL;DR: ssh -vT <host> displays where it is looking for your .ssh directory. Probably you will want check permissions and the %HOME% environment variable too. In case your job is getting stuck, click here to skip the introduction text.


  • At TupiLabs, we have repositories hosted at GitHub (public repositories) and BitBucket (mix of public and private repositories).
  • We use Jenkins for many activities. Not only as a build server, but as a function in our development environment. We will talk about that later ;-)
  • We use Jenkins, Mac and Windows for development.
  • We have jobs running at Linode with Ubuntu+Jenkins+Git Plug-in+BitBucket.
  • There aren’t many resources for configuring Jenkins and BitBucket in Windows.
  • I have a good friend of mine who would like to read about it. Heck! That’s enough to write about it :-D