Installation

Docker

The latest stable version of JLOH is available as a docker image in Docker Hub. To obtain it, make sure you have a functioning Docker Engine in your system. If that’s the case, simply run this command from your terminal:

docker pull cgenomics/jloh

First run

If everything went smoothly, you should be able to run JLOH simply by running:

docker run --rm -t -i cgenomics/jloh --help

Note

The docker image downloaded will contain all the dependencies and will function as is (no need to read further).

GitHub

The latest development version of JLOH is available in GitHub. Below find the instructions on how to proceed with the installation from GitHub.

To get the latest stable release, open the JLOH GitHub page and navigate to the releases section on the right.

Note

Once you have downloaded it, make sure you install all the dependencies listed below before using it.

To get the latest unstable (development) release, make sure you have a functioning Git Engine in your system. If that’s the case, simply clone it in the folder you prefer:

git clone https://github.com/Gabaldonlab/jloh.git

Note

Once you have downloaded it, make sure you install all the dependencies listed below before using it.

Install dependencies

These are the dependencies that jloh requires in order to function properly.

Program	Type	Version	Links
all2vcf	Program	0.7.3	https://github.com/MatteoSchiavinato/all2vcf
bedtools	Program	2.30	https://bedtools.readthedocs.io/en/latest
Biopython	Module	1.79	https://biopython.org/
ggplot2	R library	3.3.6	https://cran.r-project.org/src/contrib/Archive/ggplot2/
MUMmer	Program	3.1	https://mummer4.github.io/install/install.html
numpy	Python module	1.21.4	https://numpy.org/
pandas	Python module	1.3.5	https://pandas.pydata.org/
pybedtools	Python module	0.8.2	https://daler.github.io/pybedtools/
pandarallel	Python module	1.6.1	https://pypi.org/project/pandarallel/
pysam	Python module	0.1.7	https://pypi.org/project/pysam/
Python	Interpreter	3.6	https://www.python.org/downloads/
Rscript	Interpreter	3.6	https://cran.r-project.org/
samtools	Program	1.13	http://www.htslib.org/download/

Note

The pybedtools python module will look for the bedtools executable in the $PATH, while the pysam python module will look for the samtools executable in the $PATH. Moreover, MUMmer and its tools (e.g. nucmer) must be in the $PATH as well. The installation of MUMmer can be a bit cumbersome in certain systems, hence we recommend you proceed with conda (conda install -c bioconda mummer). This will place in the $PATH all the toolkit from the MUMmer arsenal, in particular the tools needed by JLOH to run: nucmer, delta-filter, show-snps.

First run

If everything went smoothly, you should be able to run JLOH simply by running:

./jloh --help