Installation¶
Python-only installation¶
k-seq
package can directly install from pip
(https://pypi.org/project/k-seq/):
pip install k-seq
The python-only package has most functionalities ready-to-use for count data (e.g., preprocessed count files or a CSV table). For FASTQ read joining, trimming, and deduplication, we use EasyDIVER and require additional dependencies on PANDAseq.
Complete installation¶
Option 1: install with conda
¶
We recommend to use Anaconda to create a separate k-seq environment. Or a minimal installation: Miniconda.
To crate k-seq
environment once conda in installed:
# change directory to downloaded repo
cd /to/k-seq-git-repo
# create a k-seq environment
conda create -f environment.yml
# activate k-seq environment
conda activate k-seq
# install k-seq python package
pip install k-seq