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HOW TO DOWNLOAD GMOD BASES UPDATE
HOW TO DOWNLOAD GMOD BASES CODE

sgdbulk.xml : main release configuration for tested sample.

These are the main contents of the configuration files

HOW TO DOWNLOAD GMOD BASES UPDATE

A new release needs only a minor configuration update (release number and date), and can be generated automatically if desired. Once configured for your organism(s) and project database, it is quick to generate new bulk data release files, and link into a collection of public releases. The weakness is these need detailed documentation to make it easier to tune your site's configuration.Īll of the organism and project-specific logic is in these configuration files, including output documentation, feature controls and naming, file choices. The strength is that most aspects for genome data publication, such as feature names, types, aspects of the output format, are under your project's control. Note that you don't need to supply a password, and it may be very slow.īulkfiles has extensive configurations, in a simple XML format. These commands will create a directory named GMODTools, with a directory named GMODTools in it. If you want to try out GMODTools from SVN check out using these commands: Here is a candidate release package for GMODTools:

A highly configurable tool, with data extraction and correction methods that are separate and tunable is needed to adapt to such variation in genome databases. each genome Chado database has different policy and choices with respect to feature, vocabulary and other data.

HOW TO DOWNLOAD GMOD BASES CODE

model organism projects need fairly complex and data specific configurations - moving that to config files keeps code reusable.

combine features from several Chado dbs, and add other sources that may not be in your Chado database.

convert one common feature table + dna to several output formats in one step, or repeatedly as needed.

These stages are loosely coupled - one can go back, tweak configurations and get a new output w/o redoing the complete extraction process.

process table output in stages - better debugging of steps in process, and can split processing among computers.

simple sql dump is fast, and reliable in getting all mapped features by keeping logic simple.

using simple sql to dump all db features to intermediate table allows easy checks that all features get to bulk files.

Here are some reasons we take this approach:

postprocess these table files to create the various public use formats (the time-consuming and configurable part), organized into per-chromosome files.

The feature info is simple: type, location, name/id, and a few attributes (db_xrefs.)

dump all Chado db features using simple (and quick) sql, to common intermediate table files, and chromosome dna to raw files.

Why use this package rather than using other middleware layers to Chado db - Chado XML, Chado::AutoDBI, BioPerl, ? The general logic is

Fasta sequence for each selected feature set, with headers from feature filesĪdditional genome outputs can be added with Perl adaptor packages from a Bulkfiles base adaptor object.

DNA files (full chromosomes) in raw and fasta formats.

These are current primary outputs, which are configurable to suit project needs. It produces all the contents needed for a GMOD Standard URL genome data download folder. Once tuned to your project's needs with its organism and site configurations, it can generate public data releases on a regular basis. It works with several FlyBase Chado releases, with SGDLite, and has been tested with other Chado databases. For GMA files, this will be the title embedded inside the GMA file itself, not the title of the Workshop addon it was downloaded from.Bulkfiles is a GMOD Perl package that generates Fasta, GFF3, DNA and other bulk genome annotation files from Chado databases. Strictly within the specified Workshop addon. Strictly within the folder of a mounted game specified, e.g. Only the files embedded in the currently loaded map (. are)Ĭontains content from installed addons or gamemodes.Ĭontains only the content from workshop addons. Location of the root folder (where hl2.exe, bin and etc. Strictly the game folder (garrysmod/), ignores mounting. Structured like base folder (garrysmod/), searches all the mounted content (main folder, addons, mounted games, etc)Īll Lua folders (lua/) including gamemodes and addonsĪll Lua files and subfolders (lua/) visible to the client state.Īll Lua files and subfolders (lua/) visible to the server state.Īll Lua files and subfolders (lua/) visible to the menu state. Here is a list of file search paths for use by the file library.