Installation program and documentation

[Nicklas Nordborg]

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.

[Nicklas Nordborg]

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

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

[Martin Svensson]

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

[Nicklas Nordborg]

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

Added INSTALL file

[Martin Svensson]

(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.

[Martin Svensson]

(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.

[Nicklas Nordborg]

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

Documented the need for Base2CorePlugins.jar

[Nicklas Nordborg]

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

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

[Martin Svensson]

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

[Martin Svensson]

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

[Martin Svensson]

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

[Martin Svensson]

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

[Martin Svensson]

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

[Nicklas Nordborg]

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.

[Martin Svensson]

(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.

[Nicklas Nordborg]

(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.

[Nicklas Nordborg]

(In [583]) References #89: Installation program and documentation

Minor changes to installation and readme instructions. Installation creates software item also.

[Nicklas Nordborg]

(In [585]) References #89: Installation program and documentation

Updated compiling instructions. Added a check for BASE2Core.jar and BASE2CorePlugins.jar in the build file.

[Martin Svensson]

(In [587]) References #89 Correct the name of the plug-in

[Nicklas Nordborg]

(In [626]) References #89, #100: Added formulas for better SNP gui. Gtype = ch(1), Log R Ratio = ch(2), B Allele Freq = ch(3)

[Nicklas Nordborg]

(In [627]) References #89: Installation program and documentation

Added readme for SNP data.

[Nicklas Nordborg]

(In [628]) References #89: Installation program and documentation

Made the SNP reame wikified.

[Nicklas Nordborg]

(In [629]) References #89: Installation program and documentation

Preparing for release. Added some more information to README_SNP.