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#89 closed task (fixed)

Installation program and documentation

Reported by:	Nicklas Nordborg	Owned by:	Johan Enell
Priority:	critical	Milestone:	Illumina package v1.0
Component:	net.sf.basedb.illumina	Keywords:
Cc:

Description

Create an installation program with documentation. The installation program needs to:

Add a new raw data type
Add more annotation columns to reporters
Create platform(s) and data file type(s)
Register the plug-ins
more...?

One idea is that the installation program is itself a plug-in. This would work well for the registration of platform and file types, but it still needs a manual database update to create tables/columns needed for the Illumina raw data type and reporter annotations.

Change History (24)

comment:1 by Johan Enell, 16 years ago

Milestone:	→ Illumina package v1.0

comment:2 by Nicklas Nordborg, 16 years ago

(In [549]) References #89: Installation program and documentation

Updated installation procedure to something that might actually work when BASE 2.6 is released.

comment:3 by Martin Svensson, 16 years ago

(In [551]) References #89 Start to insert illumina items with the installation plug-in

comment:4 by Nicklas Nordborg, 16 years ago

(In [553]) References #89: Installation program and documentation

Added INSTALL file

comment:5 by Martin Svensson, 16 years ago

(In [554]) References #89 Illumina items are now created by the installation plug-in but there are still some checks and testings that need to be done befor this plug-in is finished.

comment:6 by Martin Svensson, 16 years ago

(In [555]) References #89 Added more property checks when an item already exists and changed some exception messages. Now await some comments on names, ids etc. according to our meeting 25/1.

comment:7 by Nicklas Nordborg, 16 years ago

(In [557]) References #89: Installation program and documentation

Documented the need for Base2CorePlugins.jar

comment:8 by Nicklas Nordborg, 16 years ago

(In [566]) References #89: Installation program and documentation

Added rest of the plug-ins to automatic installation. Cleaned up some parts of the installation.

comment:9 by Martin Svensson, 16 years ago

(In [570]) References #89 Inserted the readme-text in wiki format.

comment:10 by Martin Svensson, 16 years ago

(In [571]) References #89 Updated svn-properties for README file

comment:11 by Martin Svensson, 16 years ago

(In [572]) References #89 Change names, ids and variables according to README

comment:12 by Martin Svensson, 16 years ago

(In [573]) References #89 Added extended properties to be used with Illumina in BASE.

comment:13 by Martin Svensson, 16 years ago

(In [576]) References #89 Changed to wiki format and configured some svn properties

comment:14 by Nicklas Nordborg, 16 years ago

What about creating Scanner (Hardware) and Software entries?

According to the README:

Scanner = Illumina BeadArray Reader
Software = Illumina BeadScan

Maybe also an entry for BeadStudio?

I think the installation program can have boolean options for this and maybe additional fields for setting the name and versions:

Create scanner: yes/no
Scanner name: Illumina BeadArray Reader
Scanner version:

...and the same for software. The default of the first parameter should be 'yes' if this is a first time installation and 'no' otherwise.

comment:15 by Martin Svensson, 16 years ago

(In [577]) References #89 Installation plug-in is now able to create Illumina scanner in the installation process. Also changed some text/options in a couple of parameters.

comment:16 by Nicklas Nordborg, 16 years ago

(In [580]) References #89: Installation program and documentation

Added 'Getting started' section to readme. Reformatted list of column mappings for reporter annotations. Minor changes to importer configurations to make them work with the HumanRef-8_V2_0_R2_11223162_A.bgx file.