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