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