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iAmphioxus

Tag Archives: Python

Using anaconda to manage local python environment

25 Thursday Jan 2018

Posted by iAmphioxus in Bioinformatics

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conda, Python

It happens that different bioinformatic tools that we want to install requires specific python library versions. What makes it worse isĀ  that sometimes the python libraries that they required could be incompatible with each other, leaving our local python environment as a messy place to manage. Anaconda is a great tool to manage local python environment and libraries. With Anaconda, we can easily create isolated virtual environment for a specific python version:

# download the latest Anaconda distribution for Linux
$ wget https://repo.continuum.io/archive/Anaconda3-5.0.1-Linux-x86_64.sh
# use conda to create a python 3.5 environment named "py35"
$ conda create -n py35 python=3.5 anaconda
# activate the py35 environment
$ source activate py35
# to verify the current active python version
$ python --version

Reference

https://conda.io/docs/user-guide/tasks/manage-python.html

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Installing Python 2.7 on the SUG@R cluster of Rice University

27 Monday Feb 2012

Posted by iAmphioxus in Bioinformatics, Blogs

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Python, Stampy

I am using a software package called Stampy to map illumina sequencing reads against the reference genome for my project. In order to install Stampy, a Python of version 2.6 or 2.7 is prerequisite. The default version of Python on our computing cluster, SUG@R, is 2.4.3 and the optional version is 3.2.1, so neither of them can work with Stampy. So I need to install Python 2.7 on SUG@R by myself. The step is as follows>> Continue reading →

29.718460 -95.402683

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Recent Posts

  • Using anaconda to manage local python environment
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