Register MIPs libraries

[Nicklas Nordborg]

This step is probably only a success/failure option with some information about date(s), operator(s), etc. Maybe we should also be able to change the barcode assignment in case the preliminary assignment made in the design wizard was changed.

There are no concentration measurements or attempts to normalize on individual libraries. This is all done on temporary or final pools.

[Nicklas Nordborg]

In 5389:

References #1133: Re-organize the Reggie front page

Added lots of wizards to the "MIPs library preparation and analysis" section. The wizards will be implemented in other tickets. See #1130, #1135, #1136, #1137, #1138 and more to come.

[Nicklas Nordborg]

In 5419:

References #1135, #1136 and #1137.

Added a counter query for some more MIPs-related wizards. A MIPs plate without a creation date is in the lib-prep process and it should show up in the "Lab protocol" wizard and in the "MIPs library registration" wizard.

[Nicklas Nordborg]

In 5425:

References #1137: Register MIPs libraries

First version of this wizard. It is more or less the same as the other library registration wizard except that no files from Qubit or Caliper are used.

The important thing here is that a creation date is registered so that the libraries and MIPs plate can move forward to the pooling step.

We also need to implement barcode assignment somewhere, either in this wizard, in the plate design wizard or as a separate wizard.

[Nicklas Nordborg]

In 5429:

References #1137: Register MIPs libraries

Added BarcodeTemplate plate type. Plates of this type is intended to hold links to Tag items (of type Barcode) via a "virtual" extract. When registering libraries for a MIPs plate a barcode template plate is also selected and each library on the MIPs plate is assigned the Barcode from the corresponding position on the template plate.

Template plates and Barcode items must currently be created manually.

[Nicklas Nordborg]

In 5437:

References #1137: Register MIPs libraries

Added Pipeline annotation to barcodes.

The installation wizard will set existing TrueSeq barcodes to RNAseq.

Changes in the LibPrepServlet will make sure that only RNAseq barcodes appear in the "Assign barcodes to cDNA plate" wizard.

Changes in DemuxJobCreator class will make sure that only the RNAseq barcodes are outputted as dummy lines in the demux sample sheet for catching library preparation errors involving mixed-up barcodes.

[Nicklas Nordborg]

In 5438:

References #1137: Register MIPs libraries

Added Pipeline annotation to BarcodeTemplate plates.

[Nicklas Nordborg]

In 5450:

References #1136 and #1137. Added some date and operator annotations that are more relevant for the MIPs pipeline (Hybridization and PCR). The lab protocols have been updated as well as the library registration wizard.