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TearDrop - Transcriptome Expression Analysis Result Drop

Please do not use yet, it's very alpha. But when it's finished all your transcriptome analysis problems will be solved.

Roadmap

doc/todo.md contains the master plan. In case you're interested in helping out, there's also doc/treasure_map.md to show you around the code and provide weak rationalizations for why I did stuff they way I did it.

Installation

Requires a sheepload of Perl modules, most prominently Mojolicious and DBIx::Class. The latter will install half of CPAN on your computer to satisfy their needs. That is not enough, however, so dependencies like Mouse, Moose and Moo (don't ask) account for the other half. I should remember to replace this with a real dependency list and possibly also fill some of the nice files that help to automagically install everything.

Whatever you think you're doing, consider using PerlBrew. You can install your favorite current Perl version and all modules without admin rights or interfering with the system perl.

After that, you can install the necessary modules like this:

> perlbrew use stable
> perlbrew install-cpanm # in case you haven't done so already
> cpanm -i Mojolicious DBIx::Class

If you don't like PerlBrew, skip steps 1 and 2 (I would still recommend using cpanm)

Database Setup

currently only tested with PostgreSQL, but DBIx::Class promises to work with anything

  1. Create teardrop database user and master database

    psql -U postgres postgres=# create user teardrop createdb; postgres=# create database teardrop_master owner teardrop;

  2. Set up master schema

Should maybe provide a script.

> psql -U teardrop teardrop_master < db/master_schema.sql

Configuration

Create skeleton config

Edit config.yml in the base directory. At the very least it needs to have the configuration for the master database

plugins:
  DBIxClass:
   default:
     dsn: dbi:Pg:dbname=teardrop_master;host=wherever
     schema_class: TearDrop::Master::Model
     user: teardrop
     options:
       RaiseError: 1
       PrintError: 1
       auto_savepoint: 1

Project databases will be configured on the fly from a table in the master schema.

Your First Project

There is a command line script to help you get started with new projects. Try

> perl bin/deploy_project.pl --help_deploy

to get a short usage message. To set up a new project, do this:

> perl bin/deploy_project.pl --create --project [shortname] --title "[display name]" -g [group]

This sets up a new project database and creates the structure and lookup tables as copies from the master schema.

Ignore the group value for now, it must be set, but is not used.

Startup

Start development instance:

> morbo -v scripts/tear_drop

Point your browser to http://localhost:3000/teardrop

You might want to create a wrapper shell script to set up paths and start TearDrop using Hypnotoad or any PSGI server (e.g. Starman). Refer to the Mojolicious Cookbook for details.

Importing Data

Please have a look at doc/importing data.md.

What now?

Annotate away!