Opened 12 years ago

Closed 11 years ago

#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 Changed 12 years ago by Johan Enell

Milestone: Illumina package v1.0

comment:2 Changed 12 years ago by 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.

comment:3 Changed 12 years ago by Martin Svensson

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

comment:4 Changed 12 years ago by Nicklas Nordborg

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

Added INSTALL file

comment:5 Changed 12 years ago by 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.

comment:6 Changed 12 years ago by 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.

comment:7 Changed 12 years ago by Nicklas Nordborg

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

Documented the need for Base2CorePlugins.jar

comment:8 Changed 12 years ago by 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.

comment:9 Changed 12 years ago by Martin Svensson

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

comment:10 Changed 12 years ago by Martin Svensson

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

comment:11 Changed 12 years ago by Martin Svensson

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

comment:12 Changed 12 years ago by Martin Svensson

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

comment:13 Changed 12 years ago by Martin Svensson

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

comment:14 Changed 12 years ago by Nicklas Nordborg

What about creating Scanner (Hardware) and Software entries?

According to the README:

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 Changed 12 years ago by 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.

comment:16 Changed 12 years ago by 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.

comment:17 Changed 12 years ago by Nicklas Nordborg

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

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

comment:18 Changed 12 years ago by 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.

comment:19 Changed 12 years ago by Martin Svensson

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

comment:20 Changed 11 years ago by 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)

comment:21 Changed 11 years ago by Nicklas Nordborg

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

Added readme for SNP data.

comment:22 Changed 11 years ago by Nicklas Nordborg

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

Made the SNP reame wikified.

comment:23 Changed 11 years ago by Nicklas Nordborg

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

Preparing for release. Added some more information to README_SNP.

comment:24 Changed 11 years ago by Nicklas Nordborg

Resolution: fixed
Status: newclosed
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