.. highlight:: none
.. _config:
Configuration
=============
This section describes how to configure Mutalyzer and includes a list of all
available configuration settings.
Mutalyzer looks for its configuration in the file specified by the
``MUTALYZER_SETTINGS`` environment variable. Make sure to always have this
environment variable set when invoking any component of Mutalyzer. One way of
doing this is by exporting it::
$ export MUTALYZER_SETTINGS=~/mutalyzer/settings.py
If you like, you can add this command to your ``~/.bashrc`` to have it
executed every time you open a shell.
Another way is by prefixing your invocations with
``MUTALYZER_SETTINGS=...``. For example::
$ MUTALYZER_SETTINGS=~/mutalyzer/settings.py mutalyzer-website
Example configuration
---------------------
If you followed the steps in :ref:`install`, this is a standard configuration
file that will work for you:
.. code-block:: python
REDIS_URI = 'redis://localhost'
DATABASE_URI = 'postgresql://mutalyzer:*****@localhost/mutalyzer'
This is not yet a minimal configuration. In fact, you can run Mutalyzer
without a configuration file since the default configuration works out of the
box. The default configuration uses a mock Redis instance, an in-memory
database backend and a temporary directory for cache and log files, so it is
not recommended for anything more than playing around.
The next section describes all available configuration settings.
Configuration settings
----------------------
Note that the configuration file is interpreted as a Python module, so you can
use arbitrary Python expressions as configuration values, or even import other
modules in it.
Unsetting a configuration setting is done by using the value `None`. If no
default value is mentioned for any configuration setting below it means it is
not set by default.
.. _config-email:
EMAIL
The email address used in contact information on the website and sent with
NCBI Entrez calls.
`Default value:` ``mutalyzer@humgen.nl``
BATCH_NOTIFICATION_EMAIL
The email address used as sender in batch job notifications. If set to
`None`, the value of :ref:`EMAIL <config-email>` will be used.
`Default value:` `None`
.. _config-debug:
DEBUG
If set to `True`, Mutalyzer runs in debug mode and will show more
information with errors.
`Default value:` `False`
.. _config-cache-dir:
CACHE_DIR
The cache directory which is used to store uploaded and downloaded files
such as reference files from the NCBI and batch job results.
`Default value:` ``/tmp``
User input settings
^^^^^^^^^^^^^^^^^^^
MAX_FILE_SIZE
Maximum size for uploaded and downloaded files (in bytes).
`Default value:` `10 * 1048576` (10 MB)
EXTRACTOR_MAX_INPUT_LENGTH
Maximum sequence length for description extractor (in bases).
`Default value:` `50 * 1000` (50 Kbp)
BATCH_JOBS_ERROR_THRESHOLD
Allow for this fraction of errors in batch jobs.
`Default value:` `0.05`
Database settings
^^^^^^^^^^^^^^^^^
DATABASE_URI
SQLAlchemy database connection URI specifying the database used to store
users, samples, variants, etcetera.
================ =============================================================
Database system Example URI
================ =============================================================
PostgreSQL ``postgresql://mutalyzer:*****@localhost/mutalyzer``
MySQL ``mysql://mutalyzer:*****@localhost/mutalyzer?charset=utf8``
SQLite ``sqlite:////tmp/mutalyzer.db``
================ =============================================================
See the SQLAlchemy documentation on
`Engine Configuration
<http://docs.sqlalchemy.org/en/latest/core/engines.html>`_ for more
information.
`Default value:` ``sqlite://`` (in-memory SQLite database)
REDIS_URI
Redis connection URI (can be any `redis-py
<https://github.com/andymccurdy/redis-py>`_ connection URI). Set to `None`
to silently use a mock Redis. Redis is only used for non-essential
features such as caching of external resources.
`Default value:` `None`
Settings for output and logging
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
All Mutalyzer messages come with a level which can be one of:
====== ======== ======================================================
Level Alias Meaning
====== ======== ======================================================
-1 Log Specifically log a message.
0 Debug Debug information.
1 Info Info.
2 Warning Regular warnings.
3 Error Serious errors that can be compensated for.
4 Fatal Errors that are not recoverable.
5 Off Can be used as a log/output level to turn off output.
====== ======== ======================================================
LOG_FILE
Name and location of the log file.
`Default value:` ``/tmp/mutalyzer.log``
LOG_LEVEL
Level of logged messages.
`Default value:` `3`
OUTPUT_LEVEL
Level of output messages.
`Default value:` `1`
LOG_TIME_FORMAT
Format of time prefix for log messages. Can be anything that is accepted as
the format argument of `time.strftime
<http://docs.python.org/2/library/time.html#time.strftime>`_.
`Default value:` ``%Y-%m-%d %H:%M:%S``
Website settings
^^^^^^^^^^^^^^^^
.. _config-reverse-proxied:
REVERSE_PROXIED
If set to `True`, the WSGI application runs behind a reverse proxy (e.g.,
nginx using ``proxy_pass``). This needs to be set if the application is
mapped to a URL other than / or a different HTTP scheme is used by the
reverse proxy.
`Default value:` `False`
.. _config-website-root-url:
WEBSITE_ROOT_URL
URL to the website root (without trailing slash). Used for generating
download links in the batch scheduler.
`Default value:` `None`
.. _config-soap-wsdl-url:
SOAP_WSDL_URL
URL to the SOAP webservice WSDL document. Used to build the WSDL document
and for linking to it from the documentation page on the website.
`Default value:` `None`
.. _config-json-root-url:
JSON_ROOT_URL
URL to the HTTP/RPC+JSON webservice root (without trailing slash). Used for
linking to it from the documentation page on the website.
`Default value:` `None`
Piwik settings
^^^^^^^^^^^^^^
`Piwik <http://piwik.org/>`_ is an Open Source analytics platform. Mutalyzer
has built-in support for visitor tracking with Piwik.
PIWIK
If set to `True`, Piwik is enabled and some Javascript tracking code is
included in every Mutalyzer website page.
`Default value:` `False`
PIWIK_BASE_URL
Base URL for the Piwik server.
`Default value:` ``https://piwik.example.com``
PIWIK_SITE_ID
Piwik site ID for Mutalyzer.
`Default value:` `1`
Miscellaneous settings
^^^^^^^^^^^^^^^^^^^^^^
LRG_PREFIX_URL
Prefix URL from where LRG files are fetched.
`Default value:` ``ftp://ftp.ebi.ac.uk/pub/databases/lrgex/SCHEMA_1_7_ARCHIVE/``
DEFAULT_ASSEMBLY
Default genome assembly (by name or alias).
`Default value:` ``hg19``
NEGATIVE_LINK_CACHE_EXPIRATION
Cache expiration time for negative transcript<->protein links from the NCBI
(in seconds).
`Default value:` `60 * 60 * 24 * 30` (30 days)
USE_RELOADER
Enable the `Werkzeug reloader
<http://werkzeug.pocoo.org/docs/0.10/serving/#reloader>`_ for the website.
This is disabled by default due to `a bug with using the reloader
<https://github.com/mitsuhiko/werkzeug/issues/461#issuecomment-139369694>`_
in combination with ``python -m mutalyzer.entrypoints.website``.
`Default value:` `False`