Implement wizards for cDNA->Library processing

[Nicklas Nordborg]

This ticket is the master ticket for the multiple wizards that are needed to process cDNA into barcoded libraries that are then put into flow cells. Further discussion is needed before we know exactly how this is going to work. So far it is similar to the RNA->cDNA wizard (#422).

1. (#456) Select a cDNA plate and possibly a subset of the cDNA items on it to process. Child plates and items are created without dates to indicate that the process has not yet been completed.
2. (#457) Generate an appropriate lab protocol
3. (#472) Generate data files needed for lab instruments so that users don't have to manually type or copy information.
4. (#473) Import results from lab instruments (eg. quality control)
5. (#473) Register the process as completed, including information about dates, operators, protocols, etc.

[Nicklas Nordborg]

(In [1804]) References #423: Implement wizards for cDNA->FlowCell? processing

Started with preparations for this batch of wizards.

• Added a new section on the main index page (links not working yet).
• Installation wizard now create 24 'TruSeqIndexXX` barcodes.
• Installation wizard rearranged to 3 columns for better space utilization. Also changed so that not all items are visible if everything is ok (if there is an error all items are visisble).

[Nicklas Nordborg]

(In [1805]) References #423: Implement wizards for cDNA->FlowCell? processing

Renamed barcodes to 'ADXXX' since that is the what Illumina is using in their product list.

[Nicklas Nordborg]

(In [1808]) References #423: Implement wizards for cDNA->FlowCell? processing

Barcode with index 17 is also missing from the kits.

[Nicklas Nordborg]

(In [1815]) References #422 and #423. Rearranged the Reggie main page since it was becoming a bit unbalanced. Moved all lab-related wizards to the left column and all administrative wizards to the right column. Added a new section for pooling and flow-cell related wizards and changed the icon for the barcoding and library preparation wizards.

[Nicklas Nordborg]

(In [1867]) References #422, #423 and other related tickets. Updated @since javadoc annotations to @since 2.12 for new methods and classes.

[Nicklas Nordborg]

(In [1899]) References #422 and #423. New name pattern for mRNA, cDNA and Library plates: MRnaPlateNNNN, CDnaPlateNNNN and LibPlateNNNN.

[Nicklas Nordborg]

(In [1918]) References #423: Implement wizards for cDNA->Library processing

Removed debug flags.

[Nicklas Nordborg]

(In [1920]) References #422, #423 and #478. Disabled links to non-working wizards in preparation for beta-release.

[Nicklas Nordborg]

(In [1924]) References #422, #423 and #478. Re-enabled links to wizards in development.

[Nicklas Nordborg]

(In [1977]) References #422, #423, #478 and more... Added Operator annotation and use it for all steps in the library preparation and pooling.

[Nicklas Nordborg]

(In [2004]) References #422, #423 and #478. Added several bioplate annotation types into categories so that they will be easier to find those that are useful for bioplates of a given bioplate type in the regular BASE interface (assuming that BASE 3.2.3 has been installed; see ​http://base.thep.lu.se/ticket/1761).

[Nicklas Nordborg]

All wizards in this category should be ok.