Tag Archives: virtualenv

conda and bioconda channel

Posted on February 23, 2016 by Thomas Cokelaer

Anaconda ( https://www.continuum.io/downloads ) provides a Python distribution with more than 400 of the most popular Python packages for science, math, engineering, and data analysis. Anaconda installs an executable called conda that will be your entry point. Anaconda solves two … Continue reading →

Posted in biology, Python | Tagged , , | 1 Comment

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 →

Posted in Python, Software development | Tagged , | 2 Comments

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 →

Posted in Python, Software development | Tagged | 6 Comments

Installing JPype to use Java from Python

Posted on October 26, 2012 by Thomas Cokelaer

JPype is a Python package that allows you to call Java from Python. First, download the zip file (I got version 0.5.4.2). I will use a virtual environment here, so the syntax is simply: cd /home/user/Downloads # path where the … Continue reading →

Posted in Linux, Python | Tagged , , , | 4 Comments

installing rpy2 with different R version already installed

Posted on January 31, 2012 by Thomas Cokelaer

The easiest way to install a python package is to use easy_install (or pip), so to install rpy2, type: easy_install rpy2 To test that it is properly installed, type: import rpy2; from rpy2 import robjects; robjects.r(“version”) If this code works, … Continue reading →

Posted in Computer Science, Linux, Python | Tagged , , , , | 8 Comments

What is Virtualenv

Posted on May 25, 2011 by Thomas Cokelaer

Virtualenv is a tool to create isolated Python environments. Its usage could be very useful when dependencies and versions are tricky. Imagine you have an application that needs version 1 of a library, but another application requires version 2. If … Continue reading →

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