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or use prove:

    prove -lrv t/

to run the Mimosa test suite.

## How do I deploy a Mimosa schema?

If you want to use Mimosa with SQLite, that is the default:

    perl script/mimosa_deploy.pl

If you want to deploy Mimosa to an already installed Chado schema, pass the --chado flag

    perl script/mimosa_deploy.pl --chado 1

This will also require you to give the proper DSN to your Chado instance in app_mimosa.conf.

If you want to use a different config file:

    perl script/mimosa_deploy.pl --chado 1 --conf my_other.conf

If you want to deploy an empty schema, because you plan to load custom sequence sets later on:

    perl script/mimosa_deploy.pl --chado 1 --empty 1 --conf some.conf

## How do I start Mimosa ?

To start Mimosa on the default port of 3000 :

    perl -Ilib script/mimosa_server.pl

If you want to run it on a specific port, then pass the -p param :

    perl -Ilib script/mimosa_server.pl -p 8080

## How do I hack on Mimosa ?

If you are developing a new feature in Mimosa, and you want start a new Mimosa
instance with the default database, there is a convenient script:

    ./scripts/debug_freshly_deployed_server.sh

That will remove mimosa.db, deploy a new mimosa_db, and start a new Mimosa
instance on port 8080 with DBIC_TRACE=1 set so every SQL statement run will be
shown.

Each new Mimosa feature should have a new test file in t/ of the form
t/NNN_feature_name.t .

## How do I configure Mimosa ?

The file called "app_mimosa.conf" contaings your configuration. In it, you can
tell Mimosa what your database backend is (SQLite, MySQL, PostgreSQL, Oracle, and
anything else that DBI supports) and set various paramters. Here is a partial list:

###  min_sequence_input_length 6

This sets the smallest sequence input length. If a sequence smaller than this length
is submitted, an exception is thrown and an error page is shown to the user.

### allow_anonymous 1

Whether to allow anonymous people (those that have not authenticated) to submit
jobs for reports.

### disable_qsub 1

Disable qsub job queueing support, which means jobs will be run on the local machine.

### tmp_dir /tmp/mimosa

The temporary directory that Mimosa can use.

### job_runtime_max		30

The default maximum time that a job can take, if it is happening during a
request cycle. Defaults to thirty seconds.

### sequence_data_dir examples/data

The directory where sequence data can be found.

### <Model::BCS>

This Config key is a container for Bio::Chado::Schema-related
configuration. It has:

### schema_class App::Mimosa::Schema::BCS

The schema class.

### traits undef

A trait, such as "Caching", which is good for production, but
not testing.

The <Model::BCS> container has a <connect_info> container,
which contains the "dsn" config key.

### dsn dbi:SQLite:./mimosa.db

The default is to deploy to a SQLite database in the current
directory, but if you want to use this with a
currently-existing Chado installation, you should but the
connection information in this config key.


## What is Mimosa written in?

Mimosa is written in Perl 5, HTML, CSS, and JavaScript.  On the server side, it
uses Moose, BioPerl and the Catalyst web framework.  On the client side, it uses
JQuery, JQuery UI.

## How can I help hack on Mimosa or otherwise get involved?

Please join our mailing list at <http://groups.google.com/group/gmod-mimosa> and
take a look at our Github issues for ideas about what we need help with:
<https://github.com/GMOD/mimosa/issues> . Please use Mimosa and tell us how we
can improve it and help it meet your sequence alignment needs.