Installation

Before using TEFLoN2, you need to install its dependencies. TEFLoN2 uses Python 3, BWA (Burrows-Wheeler Alignment Tool), Samtools, RepeatMasker, and Snakemake. It has been successfully tested on Linux/Ubuntu platforms.

TEFLoN2

TEFLoN2 can be installed from the Github repository or directly via the terminal:

$ sudo apt update
$ sudo apt install git
$ git clone https://github.com/asfistonlavie/TEFLoN2.git
$ cd TEFLoN2

Dependencies

Python ≥ 3
AWK ≥ 5.1.0
BWA ≥ 0.7.17
SAMtools ≥ 1.15
RepeatMasker ≥ 4.1.2 (optional)
Snakemake ≥ 7.7.0

Using SingularityCE (optional)

To install SingularityCE ≥ 3.11.0, follow the instructions on the official website SingularityCE site.

A Singularity container is available with all the required tools precompiled. You can build the container using the provided Singularity file in the repository:

$ sudo singularity build TEFLoN2.simg Singularity_TEFLoN2_[Custom,Annotation]

If you do not have sudo privileges:

singularity build --fakeroot TEFLoN2.simg Singularity_TEFLoN2_[Custom,Annotation]

After, to use the TEFLoN2.simg container, you have to use :

singularity exec TEFLoN2.simg snakemake --configfile config.yaml -s Snakefile -p -j $MAX_JOBS

Manual installation

For manual installation, we recommend following the installation guides provided by each tool.

Python 3

Check your current Python version:

$ python --version

If your version is < 3, install Python 3 https://www.python.org/doc/ from python.org or via terminal:

$ sudo apt update
$ sudo apt install python3

If all went well you now have python 3 on your computer.

BWA (Burrows-Wheeler Aligner)

Check your BWA version:

$ bwa

If BWA is not installed or the version < 0.7.17:

$ sudo apt update
sudo apt -y install bwa

Check the version again. If problems persist, refer to the bwa site.

SAMtools

Check your SAMtools version:

$ samtools --version

If SAMtools is not installed or is outdated (< 1.15), follow instructions on the samtools site.

RepeatMasker

To install RepeatMasker, follow installation instructions on RepeatMasker site.

Snakemake

Check your Snakemake version:

$ snakemake --version

If SnakeMake is not installed or is older than version < 7.7.0, install it following the instructions on SnakeMake site.