/ess-color

Primary LanguageC++

ESS-color

ESS-Color is a bioinformatics tool for constructing compressed representation of sets of k-mer sets.

Requirements

  • Linux operating system (64 bit)
  • GCC >= 4.8 or a C++11 capable compiler
  • Snakemake
  • Git
  • CMake 3.1+
  • ESSCompress
  • joinCounts
  • KMC

Quick start

First, install all the pre-requisites and make sure the executables are in your PATH. Then, install additional executables from source:

git clone https://github.com/amatur/ess-color
cd ess-color
bash compile.sh

You can move/copy ALL the executables in ess-color/bin to the bin directory that is already in your PATH. For instance, considering /usr/bin is already in PATH, you need to run the command mv ess-color/bin/* /usr/bin to move all executables for ESS-Color software. An alternative to moving/copying executables is adding the location of ess-color/bin to your PATH.

After compiling, set up the config.yaml. Change to the directory and use [TODO: add details of config file]

snakemake -s Snakefile.smk -j 8