Introduction
------------

This directory is the official repository of public bioinformatics 
data sets available from IFREMER research teams.

All these sets are described on the Sextant portal:
https://sextant.ifremer.fr/eng/Data/Catalogue#/search?fast=index&&any=bioinfo*

In turn, each project directory contains an appropriate README.txt
file containing a DOI to link data with a description.

Data organization
-----------------

All projects are organized in a similar way: data is distributed 
within several sub-folders all of them being named using the
EDAM Ontology (https://www.ebi.ac.uk/ols/ontologies/edam).

1/ Raw data is available from the 'data' sub-folder.

2/ Results from processing raw data is available in 'operation' sub-folder.

3/ In turn, sub-folders within 'data' and 'operation' rely on EDAM terms
depending on data type (data sub-folder) or operation type (operation
sub-folder).

Here is an example for Mass Spectrometry data set "COSELMAR" provided
by Ifremer's DYNECO research team:

dyneco/COSELMAR/
|
|--data
|   |--mass-spectrometry-data
|   |  |--negative-ion
|   |  |--positive-ion
|   |
|   |-report
|
|-- operation
    |--mass-spectrum-visualisation
    |   |-- report
    |
    |--workflows


Data retrieval for non Ifremer users
------------------------------------

(Ifremer users: DATAREF data is directly accessible from DATARMOR; i.e. do not re-download data!).

This repository of data is quite easily accessible using two protocols:

- ftp://ftp.ifremer.fr/ifremer/dataref/bioinfo/
- https://data-dataref.ifremer.fr/bioinfo/ifremer/

Using both URLs target the same storage.

Now, to download data:

1/ consider using ftp:// URL since this protocol (ftp stands for file transfer protocol) is dedicated to data transfer, so it is really faster than https.

2/ use either a command-line tool (such as wget or curl) or a UI-base tool (FileZilla or CyberDuck) to download data.


Data download example
---------------------

Suppose you are looking at this project using your web browser:

https://data-dataref.ifremer.fr/bioinfo/ifremer/lep/bazoricus-momarsat/

To download data, we first convert the https URL to the ftp one, as follows:
- from https:// URL, only consider that part: 'lep/bazoricus-momarsat'
- append that part to this URL: ftp://ftp.ifremer.fr/ifremer/dataref/bioinfo/
- you end up with: ftp://ftp.ifremer.fr/ifremer/dataref/bioinfo/lep/bazoricus-momarsat

Then, we use wget from the command line to get the entire project data:

cd /some/directory
wget -r -np -nH --cut-dirs=4 ftp://ftp.ifremer.fr/ifremer/dataref/bioinfo/lep/bazoricus-momarsat/

Command-line explained:

          -r: is for recursively download;
         -np: is for no parent ascending;
         -nH: is for disabling creation of directory having name same as URL i.e. ftp.ifremer.fr;
  --cut-dirs: is for ignoring number of parent directories; here, we use 4 to avoid creation of path 'ifremer/dataref/bioinfo/lep'; as a consequence, you will have directly the directory 'bazoricus-momarsat' within '/some/directory'