{"repo":"mobidic/SEAL","free":true,"listed":false,"github":"https://github.com/mobidic/SEAL","clone":"git clone https://github.com/mobidic/SEAL.git","description":"SEAL db - Simple, Efficient And Lite database for NGS","language":"HTML","stars":10,"topics":["bioinformatics","ngs","ngs-analysis","data-science","database","data-visualization","bioinformatics-databases","flask","flask-application","flask-sqlalchemy"],"license":"GPL-3.0","category":"databases-storage","readme_excerpt":"SEAL db - Simple, Efficient And Lite database for NGS 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 Installation To install SEAL db, first clone the repository from GitHub: SEAL db requires several dependencies to be installed, which can be done either with Conda or manually. Install dependencies With Conda To install dependencies with Conda, first install Conda if it is not already installed. Conda installation instructions can be found (here) After installing Conda, create a new environment using the environment.yml file provided with SEAL db: conda env create -f environment.yml Installing VEP If you have install all dependencies from conda you need to activate your environment by launching this command: conda activate seal 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. For conda environment: vep install -a cf -s homo sapiens -y GRCh37 -c /output/path/to/GRCh37/vep --CONVERT Plugins & Customs After installing VEP, you need to install several VEP plugins : The installation instructions for VEP plugins can be found (here). We are working on an installation script. A ","default_branch":null,"files":null,"tree":[],"storefront":"/r/mobidic","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/mobidic/SEAL/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}