Installing transposonmapper
Contents
Installing transposonmapper¶
Note
Installing the transposonmapper package is optional. When running SATAY from the docker container, transposonmapper is pre-installed.
Installing Transposonmapper from PyPi¶
For users that only require post processing analysis of the data (the bam file was already analyzed),
do use the default installation. For example pysam won’t be installed, hence Linux is not required.
pip install transposonmapper
For users that require the whole processing pipeline, do use:
pip install transposonmapper[linux]
Installing Transposonmapper from the GitHub repository¶
We recommend using conda as a virtual environment manager to isolate installed dependencies.
For users¶
git clone https://github.com/SATAY-LL/Transposonmapper.git Transposonmapper
cd Transposonmapper
conda env create --file conda/environment.yml
conda activate satay
pip install -e .
For developers¶
git clone https://github.com/SATAY-LL/Transposonmapper.git Transposonmapper
cd Transposonmapper
conda env create --file conda/environment-dev.yml
conda activate satay-dev
pip install -e .[dev]