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