Skip to content

Latest commit

 

History

History
105 lines (73 loc) · 2.98 KB

DEVELOPER.md

File metadata and controls

105 lines (73 loc) · 2.98 KB
Raw

Installing from source

Source code

The latest source code can be downloaded via Git:

git clone https://github.com/metasnv-tool/metaSNV.git

or as a zip file.

Dependencies

SNV calling:

Subpopulation calling:

Installing dependencies on Ubuntu/debian

On an Ubuntu/debian system, the following sequence of commands will install all required packages (the first two are only necessary if you have not enabled the universe repository before):

sudo add-apt-repository "deb http://archive.ubuntu.com/ubuntu $(lsb_release -sc) universe"
sudo apt-get update
sudo apt-get install libhts-dev libboost-dev

Installing dependencies using anaconda

If you use anaconda, you can create an environment with all necessary dependencies using the following commands:

conda create --name metaSNV -c bioconda boost htslib pkg-config numpy pandas
source activate metaSNV
export CONDA_ENV_PATH=$CONDA_PREFIX
export CFLAGS=-I$CONDA_ENV_PATH/include
export LD_LIBRARY_PATH=$CONDA_ENV_PATH/lib:$LD_LIBRARY_PATH

If you do not have a C++ compiler, anaconda can also install G++:

conda create --name metaSNV -c bioconda boost htslib pkg-config numpy pandas
source activate metaSNV
conda install gcc_linux-64 gxx_linux-64 
export CONDA_ENV_PATH=$CONDA_PREFIX
export CFLAGS=-I$CONDA_ENV_PATH/include
export LD_LIBRARY_PATH=$CONDA_ENV_PATH/lib:$LD_LIBRARY_PATH

For subpopulation calling, you will also need

conda install -c r r-essentials
conda install -c anaconda cairo

And several R libraries, see here and call function installOrLoadPackagesfunction() from within R. e.g.

source("installOrLoadPackages.R")
installOrLoadPackagesfunction(doInstall=TRUE, doSuppressPackageStartupMessages=FALSE)

Setup & Compilation

make

To test that all files and dependencies have been properly installed, run the following:

python metaSNV.py --help
python metaSNV_Filtering.py --help
python metaSNV_DistDiv.py --help
Rscript metaSNV_subpopr.R --help

To use one of the provided reference databases:

We recommend using genomes from ProGenomes2. The version provided here is a subset with one representative genome per species.

To download the species genome reference fasta file (ref_db) and the gene annotation file (db_ann), run the following:

wget http://swifter.embl.de/~ralves/metaSNV_reference_data/progenomes2_speciesReps_genomes.fna
wget http://swifter.embl.de/~ralves/metaSNV_reference_data/progenomes2_speciesReps_annotations.txt

These files will take approx. 25 GB of space.