add beacon-import tools

[khaled196]

Before merging please update the use. Galaxy user_preferences_extra_conf.yml with the following.

preferences:
    beacon2_account:
        description: Your own Beacon2 account
        inputs:
            - name: db_auth_source
              label: Beacon Database Authentication Source
              type: text
              required: False
            - name: db_user
              label: Beacon Database Username
              type: text
              required: False
            - name: db_password
              label: Beacon Database Password
              type: password
              store: vault
              required: False

The tool uses credentials and they should be stored in a vault

#set $db_auth_source = $__user__.extra_preferences.get('beacon2_account|db_auth_source', "")
            #set $db_user = $__user__.extra_preferences.get('beacon2_account|db_user', "")
            #set $db_password = $__user__.extra_preferences.get('beacon2_account|db_password', "")
            #if $db_user == "" or $db_password == "" or $db_auth_source == "":
                #set $db_auth_source = "admin"
                #set $db_user = "root"
                #set $db_password = "example"
            #end if
            {
                "db_auth_source": "$db_auth_source",
                "db_user": "$db_user",
                "db_password": "$db_password"
            }

[bgruening]

xref: https://github.com/usegalaxy-eu/infrastructure-playbook/pull/1271

[mira-miracoli]

Do we need to run a beacon 2 server for this? Current version is 1.8.0

[khaled196]

@mira-miracoli I am using it to connect to a local server for testing purposes. Still, if we can connect it to a well-established beacon, such as Phenogenatix or create one hosted by Galaxy, it will be better than I expected.