Commit bd2b1c01 authored by Kenzo-Hugo Hillion's avatar Kenzo-Hugo Hillion
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Start updating README

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[![pipeline status](https://gitlab.pasteur.fr/metagenomics/metagenedb/badges/dev/pipeline.svg)](https://gitlab.pasteur.fr/metagenomics/metagenedb/commits/dev)
[![coverage report](https://gitlab.pasteur.fr/metagenomics/metagenedb/badges/dev/coverage.svg)](https://gitlab.pasteur.fr/metagenomics/metagenedb/commits/dev)
Django based project to build genes catalog and tools
to play with it and contact external services.
The main motivation behind MetageneDB is to provide a support for all the analysis that are based on gene catalogs.
It is composed of both an API and a client side for visualization and interaction with the DB.
----
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### Dependencies
The application depends on different services that run independently on docker images and all of this is
orchestrated by `docker-compose`.
orchestrated by `docker-compose` locally.
Therefore to run the application you need:
......@@ -29,7 +29,7 @@ The settings of the Django server is based on the `backend/.env` file. You can c
You can of course customize more of the Django server settings in the `settings` module of metagenedb.
Now we will go through the different parts
Now we will go through the different parts.
#### Secret key
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#### Create your own DB on postgresql
The following variables have the default value:
The following variables have the default values:
```bash
DATABASE_HOST=postgresql
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### Populate the database
You have a set of scripts available within the `backend/scripts` directory that you can execute directly
from within the container. First identify the container ID corresponding to the backend with `docker ps` command. Then you can execute a bash terminal within the container and execute the scripts you want:
```bash
docker exec -it YOURCONTAINER_ID bash
root@YOURCONTAINER_ID:/code# python scripts/script.py
```
For the moment you can:
* Import all kegg orthologies with `load_kegg.py`: It directly fetch all KEGGs KO from the KEGG REST API.
* Import genes from IGC catalog from the [annotation file](ftp://ftp.cngb.org/pub/SciRAID/Microbiome/humanGut_9.9M/GeneAnnotation/IGC.annotation_OF.summary.gz). You can a small part of this annotation file in the `dev_data` folder.
> **Note**: You can also execute the scripts locally from a `pipenv shell` for instance. You need to make
sure that you change the way to log to postgres since the access is different from your machine compared to
from a container.
You have a set of scripts available that you can list via `manage.py --help`.
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```bash
snakeviz /my/file/path
```
\ No newline at end of file
```
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