Installation - Oshlack/Lace GitHub Wiki

STEP 1

Download the latest Lace software from https://github.com/Oshlack/Lace/releases

STEP 2 : EASY MODE
If you have conda/anaconda installed (or wish to do so - recommended - see below) Once you have the Lace software:

cd Lace
conda env create -f environment.yml 
conda activate lace
pip install .

If you are not currently a python user, but want python and all (this is a large amount) of its most useful scientific packages. Download Anaconda (https://www.continuum.io/downloads)

Alternatively if you just want a light-weight python package manager and don't need all the python packages: http://conda.pydata.org/miniconda.html [RECOMMENDED for non-python users]

STEP 2 : LESS EASY MODE

Enusre you have the pre-requisites:

  1. python 3 (and the necessary packages below)
  2. BLAT v.35 (Download zip file and install as per README - https://users.soe.ucsc.edu/~kent/src/).

Optionally for BLAT:
If using OSX and have homebrew setup:

brew install homebrew/science/blat

If you have conda setup:

conda install --channel https://conda.anaconda.org/bioconda blat

The packages you will require apart from python3 are (any version compatible with python3):

  • pandas
  • networkx 2.3
  • numpy
  • matplotlib

N.B Lace has an issue with networkx version 2.4, and this version should be avoided