Installation guide

SPARSE runs on Unix and requires Python >= version 2.7

hardware

  • SPASE runs best in multi-processes mode. Thus servers with at least 10-20 CPU cores were suggested.
  • >= 300 GBytes of memory is required to handle over 10 million metagenomic reads.
  • >= 500 GBytes of storage space.

System modules (Ubuntu 16.04):

  • pip
  • gfortran
  • llvm
  • libncurses5-dev
  • cmake
  • xvfb-run (for malt, optional)

3rd-party software:

  • samtools (>=1.2)
  • mash (>=1.1.1)
  • bowtie2 (>=2.3.2)
  • malt (>=0.4.0) (optional)

See requirements.txt for python module dependencies.

Installation with a Conda environment (Ubuntu)

To install SPARSE and all its dependencies in an isolated conda environment, you can use the environment file provided.

git clone git@github.com:zheminzhou/SPARSE.git
cd SPARSE/envs
conda env create -f sparse_env.yml
source activate sparse

Installation via PIP

pip install meta-sparse

Install from source files (Ubuntu)

sudo apt-get update
sudo apt-get install gfortran llvm libncurses5-dev cmake python-pip samtools bowtie2
git clone https://github.com/zheminzhou/SPARSE
cd SPARSE/EM && make
pip install -r requirements.txt

Change the parameters if needed.

Updating SPARSE

To update SPARSE, move to the installation directory and pull the latest version:

cd SPARSE
git pull