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How to Install HTSeq

Official HTSeq Installation Instructions

Erin's notes on installation on a MAC OSX machine

You can install HTSeq with either pip or conda, whichever you prefer.

Try the following…

$ pip install htseq
$ htseq-count --help

OR, if you have conda set up…

$ conda install -c bioconda HTSeq
$ htseq-count --help


If your installation or execution of the htseq-count command doesn't go smoothly, you may be missing some prerequisites.

To test whether you have these, do the following…

$ python
>>> import numpy
>>> import pysam
>>> import matplotlib
>>> quit()

If you get error messages saying that any of the following aren't installed, install them first before trying again to install HTSeq. You can install them using pip or conda.

back to Intro to HTSeq

wiki_htseq_install.txt · Last modified: 2017/11/28 08:55 by erin