Category Archives: Software development

Nice vscode extensions

Posted on October 23, 2021 by Thomas Cokelaer

Whether you are a new developer, or an expert developer, you should really consider using vscode https://code.visualstudio.com I have to admit I have been using VIM for years and I believe  will always use it. I tried some great tools … Continue reading →

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bioconda (how to build recipe locally)

Posted on March 26, 2020 by Thomas Cokelaer

Bioconda is great. From their web site, “it is a channel for the conda package manager specializing in bioinformatics software”. It provides over 7000 bioinformatics packages ready to use with conda install and over 850 contributors and 570 members who … Continue reading →

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How to update a forked repository (github)

Posted on December 11, 2014 by Thomas Cokelaer

I followed those steps and it worked like a charm using github interface assuming there was no changes between the fork and main repository Open your fork on GitHub. Click on Pull Requests. Click on New Pull Request. By default, … Continue reading →

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Moving from SVN to git: $Id:$ equivalent

Posted on December 11, 2014 by Thomas Cokelaer

In SVN (and CVS), you could include special strings such as $Id:$$Id:$ and after a commit, the revision number would appear after “Id:”, which was a convenient way to retrieve the revision for instance in a print statement. Apparently, with … Continue reading →

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Installing Python2.6 in a virtual environment

Posted on August 19, 2014 by Thomas Cokelaer

First, install python2.6 executable. see previous post if you have issues when compiling (gcc not found). Make sure you have installed python-dev with apt-get or yum. Then, following the instructions on the same topic but for Python 3 in a … Continue reading →

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Installing another Python version into virtualenv

Posted on August 16, 2014 by Thomas Cokelaer

The idea is that we do not want to install a new version of Python on the system (e.g., for testing purpose), which may interfere with your entire distribution. Instead, we want to create a virtual environment with virtualenv tool. … Continue reading →

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GIT tutorial

Posted on July 11, 2013 by Thomas Cokelaer

I finally decided to use GIT for one of my new project. I know this sounds odd given that everybody nowadays seems to use it… Having used SVN for a while the transition should be smooth though. There are a … Continue reading →

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