Skip to content

Latest commit

 

History

History
74 lines (43 loc) · 2.02 KB

README.md

File metadata and controls

74 lines (43 loc) · 2.02 KB
Raw

CoreMS Portal

CoreMS Logo

CoreMS Portal is a full-stack solution for mass spectrometry data processing of small molecule analysis. Currently, there are two workflows: molecular formulae assignment of ultra-high-resolution analysis of complex mixtures and GC-MS-based metabolomics analysis. LC-MS-based metabolomics workflows are presently under development.

Current Version

3.9.7.beta

Services:

  • PostgreSQL (Web and Data storage)
  • Redis (Task queues storage)
  • Flask and Celery ( Web framework and Task queues Client)
  • Celery (Task queues runner)

Data input formats

  • ANDI NetCDF for GC-MS (.cdf)
  • Mass List (centroid mode) (.txt)
  • Mass List (Profile mode) (.txt)
  • Thermo raw format (.raw)
  • Bruker D format (.d)

Data output formats

  • Text Files (.csv, tab separated .txt, etc)
  • JSON for workflow metadata

Local Deployment using docker-compose

  • To start download or git clone this repository :D

  • install docker for desktop

    There are two main way to start a local deployment, building from source, our using the images from docker hub.

  • To start from the pre built images, open the terminal and cd into local_app directory

    then: ( this command will build and pull the images, create the containers, volumes and network)

    docker-compose up

  • After the first deployment, and with the services running, we need to start migration and create all the database tables. Open a new terminal, cd into the local_app directory and then type:

    make init-db

    or if you don't have make installed, do this three commands:

    docker-compose exec web flask db init
docker-compose exec web flask db migrate -m "init commit"
docker-compose exec web flask db upgrade

  • Open you browser and go to http://localhost

  • To take all the services down and remove all the volumes:

    docker-compose down -v