Installation¶
Fivepseq is designed to run on Unix systems with python 2.7 or python 3.x.
Dependencies¶
To set up fivepseq, the following python packages need to be pre-installed manually using pip (if you don’t have pip you may install it as described here ).
Paste the following lines into the shell terminal:
git clone https://github.com/joshuagryphon/plastid -b develop
cd plastid
python setup.py install
pip install --upgrade numpy==1.19.5 pysam==0.19.0 cython==0.29.28
In order to enable exporting vector and portable image files, you’ll also need to have phantomjs installed as follows:
conda install phantomjs selenium pillow
Fivepseq installation¶
Clone the project from github:
git clone https://github.com/lilit-nersisyan/fivepseq.git
Navigate into the fivepseq directory and install:
python setup.py install
To check if fivepseq was installed correctly, type the following in the command line:
fivepseq --version
This should display the currently installed version of fivepseq. To display commandline arguments you may type:
fivepseq --help
Fivepseq module installation¶
In order to install fivepseq as a python module, you may use pip:
pip install fivepseq