Installation

Install via Conda environment files

Note

This is the recommended way for reproducible analyses

When installing a package via Miniconda, some of its dependecies might change from one installation to the other. To ensure the highest level or reproducibility we are now offering curated YAML files that can be used to install the stable versions of dadaist.

:warning: A list of environment files are available in the env directory, where you can download the appropriate version for your system.

# Change URL as appropriate selecting from the list in the link above
wget -O dadaist2.yaml "https://quadram-institute-bioscience.github.io/dadaist2/dadaist2-$(uname).yaml"

# You can use mamba instead of conda for faster installation
conda env create --file dadaist2.yaml -n dadaist2

Install via Miniconda

The easiest way to install dadaist2 is from the BioConda repository. This requires Miniconda installed (how to install it). We will first install mamba, that makes the installation faster (naturally you can skip the mamba installation if you already use it).

conda install -y -c conda-forge mamba
mamba install -y -c conda-forge -c bioconda dadaist2

If you want to keep dadaist2 and its dependencies in a separate environment (recommended):

conda install -y -c conda-forge mamba
mamba create -n dadaist -c conda-forge -c bioconda dadaist2
# Then type `conda activate dadaist` to use it

Developmental snapshot

We recomment to use Miniconda also to test the last developmental snapshot, as Miniconda can create an environment with all the required dependencies, then the binaries from the repository can be used instead:

mamba create -n dadaist-last -c conda-forge -c bioconda --only-deps dadaist2-full
git clone https://github.com/quadram-institute-bioscience/dadaist2
export PATH="$PWD"/dadaist2/bin:"$PATH"

Docker image

Dadaist2 is available from DockerHub and the image can be pulled via:

sudo docker pull andreatelatin/dadaist2:last

Advanced topics

Singularity definition

To manually build an image with the latest version from Bioconda the following definition file can be saved as dadaist-stable.def:

Bootstrap: docker
From: centos:centos7.6.1810

%environment
    source /opt/software/conda/bin/activate /opt/software/conda_env
    export PATH=/opt/software/dadaist2/bin:$PATH
    PERL5LIB=''
    LANG=C
         
%post
    yum -y install epel-release wget which nano curl zlib-devel git free
    yum -y groupinstall "Development Tools"
    mkdir -p /opt/software
    cd /opt/software    
    curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh 
    sh ./Miniconda3-latest-Linux-x86_64.sh -p /opt/software/conda -b
    /opt/software/conda/bin/conda install -y mamba
    /opt/software/conda/bin/mamba create -c conda-forge -c bioconda  -c aghozlane -p /opt/software/conda_env -y dadaist2-full cutadapt=3.3 qax  r-gunifrac 

%runscript
    exec dadaist2 "$@"

and the image built as:

sudo singularity build dadaist2.simg dadaist2-stable.def

Developmental snapshot via Singularity

To get the latest code from the repository (and also some databases) here we share a dadaist2-dev.def file:

Bootstrap: docker
From: centos:centos7.6.1810

%environment
    source /opt/software/conda/bin/activate /opt/software/conda_env
    export PATH=/opt/software/dadaist2/bin:$PATH
    PERL5LIB=''
    LANG=C
         
%post
    yum -y install epel-release wget which nano curl zlib-devel git free
    yum -y groupinstall "Development Tools"
    mkdir -p /dadaist_databases/
    mkdir -p /opt/software
    cd /opt/software  
    curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh 
    sh ./Miniconda3-latest-Linux-x86_64.sh -p /opt/software/conda -b
    /opt/software/conda/bin/conda config --add channels defaults
    /opt/software/conda/bin/conda config --add channels conda-forge
    /opt/software/conda/bin/conda config --add channels bioconda
    /opt/software/conda/bin/conda install -y mamba
    /opt/software/conda/bin/mamba create  -c aghozlane -p /opt/software/conda_env -y dadaist2-full cutadapt=3.3 qax  r-gunifrac 
    source /opt/software/conda/bin/activate /opt/software/conda_env
    cd /opt/software
    git clone https://github.com/quadram-institute-bioscience/dadaist2
    ./dadaist2/bin/dadaist2-getdb -d "dada2-unite" -o /dadaist_databases/
    ./dadaist2/bin/dadaist2-getdb -d "decipher-silva-138" -o /dadaist_databases/

%runscript
    exec dadaist2 "$@"

and the image built as:

sudo singularity build dadaist2-dev.simg dadaist2-dev.def

Docker file

To build an image with the latest version from Bioconda the following definition file can be saved as Dockerfile:

Bootstrap: docker
From: centos:centos7.6.1810

%environment
    source /opt/software/conda/bin/activate /opt/software/conda_env
    export PATH=/opt/software/dadaist2/bin:$PATH
    PERL5LIB=''
    LANG=C
         
%post
    yum -y install epel-release wget which nano curl zlib-devel git free
    yum -y groupinstall "Development Tools"
    mkdir -p /opt/software
    cd /opt/software    
    curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh 
    sh ./Miniconda3-latest-Linux-x86_64.sh -p /opt/software/conda -b
    /opt/software/conda/bin/conda install -y mamba
    /opt/software/conda/bin/mamba create -c conda-forge -c bioconda  -c aghozlane -p /opt/software/conda_env -y dadaist2-full cutadapt=3.3 qax  r-gunifrac 

%runscript
    exec dadaist2 "$@"

and the image built as:

sudo singularity build dadaist2.simg dadaist2-stable.def

Developmental snapshot with Docker

To get the latest code from the repository (and also some databases) here we share a dadaist2-dev.def file:

Bootstrap: docker
From: centos:centos7.6.1810

%environment
    source /opt/software/conda/bin/activate /opt/software/conda_env
    export PATH=/opt/software/dadaist2/bin:$PATH
    PERL5LIB=''
    LANG=C
         
%post
    yum -y install epel-release wget which nano curl zlib-devel git free
    yum -y groupinstall "Development Tools"
    mkdir -p /dadaist_databases/
    mkdir -p /opt/software
    cd /opt/software  
    curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh 
    sh ./Miniconda3-latest-Linux-x86_64.sh -p /opt/software/conda -b
    /opt/software/conda/bin/conda config --add channels defaults
    /opt/software/conda/bin/conda config --add channels conda-forge
    /opt/software/conda/bin/conda config --add channels bioconda
    /opt/software/conda/bin/conda install -y mamba
    /opt/software/conda/bin/mamba create  -c aghozlane -p /opt/software/conda_env -y dadaist2-full cutadapt=3.3 qax  r-gunifrac 
    source /opt/software/conda/bin/activate /opt/software/conda_env
    cd /opt/software
    git clone https://github.com/quadram-institute-bioscience/dadaist2
    ./dadaist2/bin/dadaist2-getdb -d "dada2-unite" -o /dadaist_databases/
    ./dadaist2/bin/dadaist2-getdb -d "decipher-silva-138" -o /dadaist_databases/

%runscript
    exec dadaist2 "$@"

and the image built as:

sudo singularity build dadaist2-dev.simg dadaist2-dev.def

Provided scripts

dadaist2 will install the following programs:

  • dadaist2, the main program
  • dadaist2-..., a set of wrappers and tools all using the dadaist2- prefix to make them easy to find (using TAB)