HTSeq 0.10.0

Table of Contents

• HTSeq 0.10.0
  • Basic information
  • Prerequisites
  • Installation
  • Mode of use
  • References
  • Author

Basic information

• Instalation date: 12/07/2018
• Official Website: https://htseq.readthedocs.io/en/release_0.10.0/
• Supercomputer: Cronos
• License: GNU General Public License

Prerequisites

• Python 2.7, Python 3.4 o superior
• numpy
• Pysam
• matplotlib (Just in case you want to generate graphics)

Installation

1. Charge Conda’s environment:

   $ conda create --name <envName> python=3.6
   $ source activate <envName>
   

2. Install numpy in the environment

   $ conda install numpy
   

3. Install Pysam:

   $ conda config --add channels r
   $ conda config --add channels bioconda
   $ conda install pysam
   

4. Download the official HTSeq repository (Source code - tar.gz) [1]

   $ cd /home/mgomezzul/apps/
   $ git clone https://github.com/simon-anders/htseq.git
   

5. Install HTSeq with the corresponding conda environment active:

   $ cd htseq/
   $ python setup.py build
   $ python setup.py install
   

In this way HTSeq is installed in the Conda environment, and added to the Conda Python path.

Mode of use

$ source activate <envName>

This will load the Conda environment and the HTSeq routes will be added to the Path.

References

[1]	https://github.com/simon-anders/htseq

Author

Andrés Felipe Zapata Palacio