requirements and installation

requirements

  • Python >= 3.5
  • HTSeq package

Note

HTSeq uses pysam package for processing alignment files. Please consult HTSeq manual and pysam manual for requirements of both packages.

installation

quick installation

If a user has a local python environment with all the dependencies for HTSeq and pysam installed, then htseq-clip can be installed as:

$ pip install htseq-clip

conda environment

We strongly encourage the use of conda package management system for multiple Python versions/various incompatible package installations. Please install conda on your computer following the guidelines. Once conda installation is successful, create a new htseq-clip enviroment as:

(base) $ conda create -n htseq-clip

and activate the environment:

(base) $ conda activate htseq-clip

now install the dependencies:

(htseq-clip) $ conda install -c bioconda pysam
....
(htseq-clip) $ conda install -c bioconda htseq

now htseq-clip can be installed in this environment as:

(htseq-clip) $ pip install htseq-clip