Update README

README.md

@@ -1,118 +1,141 @@
 # SEAL db - Simple, Efficient And Lite database for NGS
 
+![seal.gif](docs/img/seal.gif)
+
+SEAL db is a Python project that provides a simple, efficient, and lightweight
+database for Next Generation Sequencing (NGS) data. SEAL db is built with the
+Flask framework and uses PostgreSQL as the backend database. It includes a web
+interface that allows users to upload and query NGS data.
+
+__Please report any issue [here](https://github.com/mobidic/SEAL/issues/new)__
+
 ## Installation
 
-First of all clone the repo :
+To install SEAL db, first clone the repository from GitHub:
+
 ```bash
 git clone https://github.com/mobidic/seal.git
 ```
 
+SEAL db requires several dependencies to be installed, which can be done either
+with Conda or manually.
+
 ### Install dependencies
 
 #### With Conda
 
-Please install conda ([documentation here](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html))
+To install dependencies with Conda, first install Conda if it is not already installed. Conda installation instructions can be found ([here](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html))
+
+After installing Conda, create a new environment using the environment.yml file
+provided with SEAL db:
 
 `conda env create -f environment.yml`
 
-#### VEP
+#### Installing VEP
 
 > __If you have install all dependencies from conda you need to activate your
-environment by launching this command :__ `conda activate seal`
+environment by launching this command:__ `conda activate seal`
 
-You need to complete VEP installation (https://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#installer) :
-`vep_install -a cf -s homo_sapiens -y GRCh37 -c /output/path/to/GRCh37/vep --CONVERT`
+After installing dependencies, you need to install VEP (Variant Effect
+Predictor), which is used by SEAL db to annotate variants. The installation
+instructions for VEP can be found
+[here](https://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#installer).
+
+For conda environment:
 
-##### Plugins
+`vep_install -a cf -s homo_sapiens -y GRCh37 -c /output/path/to/GRCh37/vep --CONVERT`
 
-Install VEP plugins (https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html) :
+After installing VEP, you need to install several VEP plugins that are used by
+SEAL db:
   - dbNSFP
   - MaxEntScan
   - SpliceAI
   - dbscSNV
   - GnomAD
 
+The installation instructions for VEP plugins can be found ([here](https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html)).
+
 *__A more complete guide will be written soon__*
 
-### Configuration of the app
+### Configuration
+
+After installing dependencies and VEP, you need to configure the app by editing
+two files:
+- `seal/static/vep.config.json`
+- `seal/config.yaml`
 
-- Please edit file `seal/static/vep.config.json` and replace those variable:
-  - `{dir_vep}` => `/path/to/vep`
-  - `{dir_vep_plugins}` => `/path/to/vep/plugins`
-  - `{GnomAD_vcf}` => `/path/to/gnomad.vcf`
-  - `{fasta}` => `/path/to/genome.fa.gz`
+In `seal/static/vep.config.json`, replace the following variables with the appropriate paths:
+- `{dir_vep}` => `/path/to/vep`
+- `{dir_vep_plugins}` => `/path/to/vep/plugins`
+- `{GnomAD_vcf}` => `/path/to/gnomad.vcf`
+- `{fasta}` => `/path/to/genome.fa.gz`
 
-- Please edit file `seal/config.yaml` :
-  - create your secret app key.
-  - you can edit following what you need
+In `seal/config.yaml`, create your secret app key and edit other settings as
+needed.
 
-### Initialise Database
+### Initialization of the database
 
 > If you install all dependencies with conda make sure to activate the
 > environment :
 > ```bash
 > conda activate seal
 > ```
 
-> __This section is a bit tricky. We work on it to simplify the process.__
+> comment line on `seal/__init__.py` (see [#26](https://github.com/mobidic/SEAL/issues/26))
+> ```python
+> # from seal import routes
+> # from seal import schedulers
+> # from seal import admin
+> ```
+
+To initialise the database, start the database server and run the following
+commands:
 
-- Start database server
 ```bash
 initdb -D ${PWD}/seal/seal.db
 pg_ctl -D ${PWD}/seal/seal.db -l ${PWD}/seal/seal.db.log start
+python insertdb.py
+flask --app seal --debug db init
+flask --app seal --debug db migrate -m "Init DataBase"
 ```
-- Issue [#26](https://github.com/mobidic/SEAL/issues/26)
-  - comment line on `seal/__init__.py`
-  ```python
-  # from seal import routes
-  # from seal import schedulers
-  # from seal import admin
-  ```
-- Initialize database
+
+> uncomment line on `seal/__init__.py` (see [#26](https://github.com/mobidic/SEAL/issues/26))
+> ```python
+> from seal import routes
+> from seal import schedulers
+> from seal import admin
+> ```
 
 The database will be intialise with an admin user :
-  - username : `admin`
-  - password : `password`
-```bash
-python insertdb.py
-flask db init
-flask db migrate -m "Init DataBase"
-```
-- __[Optional]__ Add Gene as Region (usefull to create _in-silico_ panels)
+- username : `admin`
+- password : `password`
+
+Optionally, you can also add gene regions and OMIM data to the database.
+
 ```bash
 wget -qO- http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/ncbiRefSeq.txt.gz   | gunzip -c - | awk -v OFS="\t" '{ if (!match($13, /.*-[0-9]+/)) { print $3, $5-2000, $6+2000, $13; } }' -  | sort -u > ncbiRefSeq.hg19.sorted.bed
 python insert_genes.py
 ```
-- __[Optional]__ Add OMIM (for transmission and relative diseases) __/!\ YOU NEED AN OMIM ACCESS TO DOWNLOAD FILE__
 ```bash
 wget -qO- https://data.omim.org/downloads/{{YOUR API KEY}}/genemap2.txt
 python insert_OMIM.py
 ```
-- Issue [#26](https://github.com/mobidic/SEAL/issues/26)
-  - uncomment line on `seal/__init__.py`
-  ```python
-  from seal import routes
-  from seal import schedulers
-  from seal import admin
-  ```
 
-### Launch the app
+### Launching the App
 
-Now you can launch the app :
+Finally, to launch the app, run the following command:
 ```
 flask --app seal --debug run
 ```
 
-__Please report any issue [here](https://github.com/mobidic/SEAL/issues/new)__
-
 ## Tips & Tricks
 
-Here are listed some usefull *Tips & Tricks*.
+Here are some useful *Tips & Tricks* working with SEAL:
 
 - Update database
 ```bash
-flask db migrate -m "message"
-flask db upgrade
+flask --app seal --debug db migrate -m "message"
+flask --app seal --debug db upgrade
 ```
 - Start/Stop the datatabase server
 ```bash