Requirements

Jovian has minimal system requirements, it is intended for powerful servers and/or grid-computers but also works on powerful PCs and laptops. It has one major software dependencies: miniConda. During the installation procedure you will be asked if you want to automatically install miniconda (if it is not already available). Additionally, it depends on the following software, but most Linux systems have these pre-installed already. Any metagenomics analysis, Jovian included, depends on several public databases that you have to download.

System requirements

We have developed and tested the software for the following Linux distributions ("distro's"): RHEL, CentOS and Ubuntu. We do expect Jovian to work on other Linux distro's, but cannot guarantee stability. Incidentally, it also works on Windows Subsystem for Linux but this functionality is currently not guaranteed.

The software does not require root and/or sudo-rights. It is however necessary to have read and write access to the /tmp folder on your system. This won't be a problem most of the time since the /tmp folder is usually free to read from and write to. However, it is best to check this with your system administrator(s).

The databases require up to 400GB of disk-space. Installation of the Jovian pipeline totals ~6GB disk-space and is spread over two locations:

1. In the users' home directory*: A "Jovian_master" environment of ~2GB is installed, this serves as the "head" of the pipeline. Also, a "Jovian_helper" environment is installed to facilitate ancillary operations (e.g. database updating) which also requires ~1GB. * _{Technically it is installed in Conda's default directory, but for most users this will be home.}
   If Conda is not installed on the system, Jovian will do that automatically in the home directory, requiring ~1GB of disk-space.
2. At the location where the repo was downloaded: Here the "body" of the pipeline is installed, including all Conda software environments. It requires 4GB of disk-space.

Software requirements

The software listed below are usually pre-installed on Linux systems.

Software name	Website
git	https://git-scm.com/downloads
curl	https://curl.haxx.se/
which	http://savannah.gnu.org/projects/which
bzip2	http://www.bzip.org/

Databases requirements

Please see here for instructions about automatic downloading and configuration of required databases.

Database name	Link	Installation instructions
NCBI NT & NR	ftp://ftp.ncbi.nlm.nih.gov/blast/db/	link
NCBI Taxdump	ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/	link
NCBI New_taxdump	ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/	link
Virus-Host interaction database	http://www.genome.jp/virushostdb/note.html	link
Latest Human Genome*	https://support.illumina.com/sequencing/sequencing_software/igenome.html	link

* We suggest the latest human genome because Jovian is intended for clinical samples. You can however use any reference you'd like, as explained here.