Installation

Linux

The easiest way to install and run vtam is via conda (https://docs.conda.io/projects/conda/en/latest/index.html) environment. Download and install Miniconda https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html. Use 3.X python version.

Create a conda environment.

conda create --name vtam python=3.7 -y

Activate the conda environment.

conda activate vtam

Install Cutadapt, VSEARCH and BLAST in the environment

conda install -c bioconda blast
conda install -c bioconda vsearch

Install VTAM via pip

pip install vtam

You can also verify the BLAST (>= v2.2.26), CutAdapt (>= 3.0) and VSEARCH (>= 2.15.0) versions:

blastn -version
cutadapt --version
vsearch --version

Singularity

We provide a singularity container in the VTAM github: https://github.com/aitgon/vtam . First you build the image with this command as root:

sudo singularity build vtam.sif vtam.singularity

Then you can use VTAM directly from the singularity image:

singularity run --app vtam vtam.sif --help
singularity run --app vtam vtam.sif merge --help

Windows

You can run VTAM on a windows machine using the Windows Subsystem for Linux (WSL)

Install Windows Subsystem for Linux and Ubuntu following these instructions: https://docs.microsoft.com/en-us/windows/wsl/install-win10

Open WSL Ubuntu in a terminal and install conda using Linux instructions: https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html

If it has not been done, you need to install make and gcc:

sudo apt-get update
sudo apt install make
sudo apt-get install gcc
conda update -n base -c defaults conda

Go on with the VTAM installation as described here Linux

Note

You can access your files Windows system from the /mnt directory of your WSL. For example, execute the following command from the Ubuntu terminal to copy the file.txt from c:tempfile.txt to your current directory in WSL:

cp /mnt/c/temp/file.txt ./file.txt

Test your VTAM installation

You can verify the installation of vtam by looking at the VTAM version

cd vtam
conda activate vtam
vtam --version

The vtam example command downloads the example files and create a file structure. A snakemake command will run the whole pipeline. If you get through without an error message your VTAM installation is fully functional.

vtam example
cd example
snakemake --printshellcmds --resources db=1 --snakefile snakefile.yml --cores 4 --configfile asper1/user_input/snakeconfig_mfzr.yml --until asvtable_optimized_taxa