Installation¶
Requirements¶
To generate files needed:
- minimap2 (required to create required input PAF file)
- miniasm (required if NG(X) plots requested)
For the calculation step:
- C++ compiler with C++11 support
For the report generation step:
- Python 2.7.11
- setuptools - required for installation
- BioPython
- matplotlib v2.0.0
Installing the latest code from github¶
git clone --recursive https://github.com/simpsonlab/preqc-lr.git
cd preqc-lr
make
Installing dependencies¶
First we need to make sure we have everything to properly use pip or the setup.py script.
# create virtual environment
virtualenv preqclr-venv
source preqclr-venv/bin/activate
# check that you are using correct environment
which pip
# check that setuptools is installed
pip freeze
# update setuptools if needed
python -m pip install --upgrade pip setuptools
# check that we are using the right version of python (2.7.11+)
python -V
Okay, we are ready to install dependencies.
# download report script dependencies
python setup.py install
# OR we can use pip
pip install preqc-lr
To check that we have installed all the packages and the right versions we run pip freeze and we should see the following:
biopython==1.70
cycler==0.10.0
functools32==3.2.3.post2
gevent==1.3a1
greenlet==0.4.13
matplotlib==2.0.0
numpy==1.14.0
preqc-lr==2.0
pyparsing==2.2.0
python-dateutil==2.6.1
pytz==2017.3
six==1.11.0
subprocess32==3.5.0rc1