From 521d0b0e3f50eef70fa110c086402900549c4dfd Mon Sep 17 00:00:00 2001 From: Celine Mercier Date: Wed, 4 Sep 2019 17:19:09 +0200 Subject: [PATCH] Update home --- home.md | 61 +++++++++++++++++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 59 insertions(+), 2 deletions(-) diff --git a/home.md b/home.md index 42204e4..898ce75 100644 --- a/home.md +++ b/home.md @@ -1,3 +1,60 @@ -The OBITools3 will be available soon... +The OBITools3 are now available to download from git, and should soon be on PyPI. -[Wolf tutorial](Wolf_tutorial) \ No newline at end of file +Tutorial: +[Wolf tutorial](Wolf_tutorial) + +### Installing the OBITools3 + +Requirements: **python3, python3-venv, git, CMake** + +Then you can do: + + git clone https://git.metabarcoding.org/obitools/obitools3.git + cd obitools3 + python3 -m venv obi3-env + . obi3-env/bin/activate + pip install cython + python setup.py install + +And test the installation with: + + obi test + +### The OBITools3 data structure + +The OBITools3 rely on an ad hoc database system, inside which all the data that a DNA metabarcoding experiment must consider is stored: the sequences, the metadata (describing for instance the samples), the database containing the reference sequences used for the taxonomic annotation, as well as the taxonomic databases. + +DNA metabarcoding data can easily be represented in the form of tables, and each command can be regarded as an operation transforming one or several 'input' tables into one or several 'output' tables, which can be used by the next command. + +The new database system used by the OBITools3 (called **DMS** for Data Management System) relies on **column**-oriented storage. Each column contains a data element, and several columns can be assembled in **views** representing the data tables (equivalent to a fasta file). + +### The OBITools3 syntax + +* Basic syntax: + + obi command [options] input_URI output_URI + +* A URI (Uniform Resource Identifier) is a simple way to identify the input and output of a command. For a file, it's simply the path to the file. For a view, it can be the path to the view file in the DMS: + + path_to_my_dms.obidms/VIEWS/my_view.obiview + + Or a simplified version: + + path_to_my_dms/my_view + + Any hybrid of those 2 works too. + +* View names must be unique within a DMS, in other words, views can not be overwritten. + +* All tools accept different input and output DMS. + +* If the output DMS is not given, the input DMS is used. + +* For a taxonomy, both those and their hybrids work: + + path_to_my_dms.obidms/TAXONOMY/my_taxonomy + path_to_my_dms/taxonomy/my_taxonomy + +* `obi -h` gives a list of all the commands. + +* `obi command -h` prints the help of the command.