Installation Manual

This manual walks you through the Annot installation process of the USR user and DEV development version and teaches you how to keep annot up and running for your laboraroy.

DEV version note

I got a dev version successful running on MacOSX. I did not get it running on our Ubuntu and CentOS server. Main reason for this is, that I not was able to properly link a host directories into a docker container (step 7).

Installation Steps

  1. Install Docker and get familiar with it as described in the Docker Basics Manual part of the Annot manual.

  2. On the host machine install Git. How will depend on the flavor of the operating system you are running.

  3. Get the Annot source code from the main fork. Alternatively you can clone Annot form your own fork. In this case I assume you know what you do. Forking the prj is not described here.

    git clone  https://gitlab.com/biotransistor/annot.git
    
  4. The cloned source code’s annot/pgsql.env file contains environment variables for the PostgreSQL database. Edit the DB_PASS entry.

    DB_NAME=postgres
    DB_USER=postgres
    DB_PASS=some_strong_postgresql_root_user_password`~!@#$%^&*()-+=:;<,>.?/"
    DB_SERVICE=db
    DB_PORT=5432
    
  5. Generate a BioPortal bioontology.org account . Go to your BioPortal account settings to figure out your API application interface key.

  6. optional: Generate a synapse account, if you plan do deploy your investogationa and studies on synaps. Synapse synapse.org account . Go to your Synapse account settings to figure out your API application interface key.

  7. The crowbar.py file contains Django framework and Annot related environment variables. Write a plain text crowbar.py file with the following content. Adapt the content inside the double quotes.

    SECRET_KEY = "about_64_characters_long`~!@#$%^&*()-+=:;<,>.?/"
    PASSWD_DATABASE = "some_strong_postgresql_annot_user_password`~!@#%^&*?"
    APIKEY_BIOONTOLOGY = "your_BioPortal_bioontology.org_API_key"
    #APIKEY_SYNAPSE = "your_synapse.org_API_key"
    URL = "http://192.168.99.100/"
    CONTACT = "you@emailaddress"
    

    Place this file under annot/web/prjannot/crowbar.py .

That’s all.