Setup and system requirements¶
Note
Provided command-line examples are given as examples and are valid for a standard unix bash terminal.
Operating system and system resource¶
Operating system¶
RST4ABM was designed on Ubuntu 18.04 (Linux) but should compatible with all system capable of installing the dependencies listed on this page.
RAM memory¶
Some tools embedded in RST4ABM can be quite demanding on RAM memory. The actual requirement depends on your dataset and is influenced by parameters set in the config file. The bottleneck usually is the taxonomic assignment. Factors which can increase the RAM requirement are:
the number of samples
the bacterial diversity within your samples
the number of cores
Hint
In practice, 16 to 32 GB are usually required.
Software dependencies¶
Git¶
What for?¶
Git is required to download (clone) RSP4ABM.
Install¶
Git is available by default in operating systems. If not, follow the indications on the git installation page..
Test¶
To test if git is installed:
# To test if git is installed, make it print its version. It will fail if it is not installed
$ git --version
Conda¶
What for?¶
Conda is a convenient python-based package and environment manager. It enables the easy installation of Snakemake. Furthermore, it can be used (as an alternative to Singularity containers) by Snakemake to retrieve all the packages required for the execution of the RSP4ABM.
Test¶
To test if Conda is installed:
# To test if Conda is installed, make it print its version. It will fail if it is not installed
conda --version
Snakemake¶
What for?¶
RSP4ABM is a Snakemake 1 pipeline. Then, it must be installed and available for each execution of the pipeline.
Install¶
Follow indications on Snakemake installation page. It is good practice to create a dedicated Conda environment for Snakemake.
To install Snakemake in a dedicated “Snakemake” environment:
# Install snakemake in a environment named "Snakemake"
conda create -c bioconda -n snakemake snakemake
Test¶
To test if Snakemake is installed:
# To test if Snakmeake is installed, make it print its version. It will fail if it is not installed
snakemake --version
Singularity¶
What for?¶
Singularity is a container plateform. Its enables to create, retrieve and install containers, which are predefined transposable sets of software. The installation of Singularity is optional for most of the functions in RSP4ABM. Indeed, the user can choose when executing the pipeline between Conda or Singularity to retrieved all the required tools. Yet, it recommended to run RSP4ABM with Singularity containers since it enables the best level of reproducibility 2.
Install¶
Follow indications on Singularity installation page
Test¶
To test if Singularity is installed:
# To test if Singularity is installed, make it print its version. It will fail if it is not installed
singularity --version
Clone RSP4ABM¶
Once all dependencies installed and working, RSP4ABM can be cloned with git:
git clone https://github.com/metagenlab/microbiome16S_pipeline.git
Please note the path of the directory in which you cloned RSP4ABM since you will have to indicate it when executing the pipeline.
Reference database¶
The very last step of setup and before the first execution of the pipeline, a dedicated workflow must be executed to prepare and format the reference taxonomy database. For this, refer to Taxonomic reference database preprocessing.