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