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Bioconductor Support Site

How to customize the site

To load up different templates Biostar needs to be told which paths to look for when looking for template files. Files are loaded by name up in the order that they have been found in the path.

First investigate the settings file:

https://github.com/biostars/support.bioconductor.org/blob/rollBack/org/bioconductor/bioc_settings.py

Note how all settings are loaded from the main settings first, then some settings are customized.

Steps

The directory that the settings file is located must be importable via Python.

  1. Edit and apply the PYTHONPATH to inform Python of where to look for modules.

    Example:

     export PYTHONPATH=/home/lori/a/support.bioconductor.org/org/bioconductor:$PYTHONPATH

    Test that the settings is file is importable via

     python -m bioc_settings

    This must work from any location not just the folder that contains bioc_settings.py

  2. Now enable the new module by telling biostar which settings module to use:

     export DJANGO_SETTINGS_MODULE=bioc_settings

  3. Run biostar.sh with:

     ./biostar.sh run

    You should see a message that indicates that the base template is now loading from the starbase.html file located in

    rather than the original location

    The templates in the org directory may be modified in any way that is needed.

Custom settings

All custom settings should import from the main settings:

from biostar.settings.base import *

Within this new file users need to only override only the settings that are to be changed.

Customizing templates

Templates that are to be modified need to be copied to a new directory. Example from:

biostar/server/templates

directory to:

org/bioconductor/templates

so that it retains the same relative path. If the template was located in a subdirectory of the templates directory this same subdirectory would need to be created in the new location as well.

Template paths

To activate the Bioconductor templates users need to ensure that

org/bioconductor/templates

directory is listed ahead of the other directories in TEMPLATE_DIRS variable. For example in the custom settings module:

TEMPLATE_DIRS = [THEME_PATH] + list(TEMPLATE_DIRS)

Enabling the new settings

Run biostar in an environment where the new file is listed as a python module name (not file name) or the DJANGO_SETTINGS_MODULE environment variable

# The file is called foo.py
export DJANGO_SETTINGS_MODULE=foo

The settings file must be located in a directory that Python can import. This can be achieved by adding the directory that stores the new settings file to the Python path:

# The full path is /home/biostar/bar/foo.py
export PYTHONPATH=/home/biostar/bar:$PYTHONPATH
export DJANGO_SETTINGS_MODULE=foo

Environment variables

Biostar may be customized via a number of environment variables that otherwise have default values. Export an environment variable with the given name to override a setting. Default values:

DJANGO_SETTINGS_MODULE = biostar.settings.base
BIOSTAR_ADMIN_NAME = Biostar Admin
BIOSTAR_ADMIN_EMAIL = [email protected]
SECRET_KEY = [email protected]
EMAIL_HOST = localhost
EMAIL_PORT = 25
EMAIL_HOST_USER = postmaster
EMAIL_HOST_PASSWORD = password

These settings are for convenience only. The custom settings file that a user creates may choose to directly specify any of these settings.