= Updating to Reggie 2.13 =

'''IMPORTANT! ''' Before installing this update, there are a number of things that need to be checked and manually fixed!!!

=== 1. Make sure that pools have been registered ===

Make sure that all created pools have been completed in the lab and registered. Eg. the '''Lab protocols for pooling''' and '''Register pooled libraries''' wizards should display (0) items waiting for registration. Otherwise the lab protocols will show incorrect mixing values.

=== 2. Flag some libraries and their parent RNA item ===

Due to a bug (see #508), libraries which got a Qubit concentration measurement of '''0 ng/µl''' have been left in a dead end state. To ensure that new RNA is extracted in the future, a flag must be set manually and the parent RNA items must be added to the '''Flagged RNA''' list. 

 1. To find the libraries in question go to the '''Biomaterial LIMS->Extracts''' page and filter on '''Type=Library''' and '''CA_Molarity=0'''.
 2. Edit each library item and set the annotation: '''Flag=!ExcludedFromPool'''.
 3. Find the parent RNA item for each library and set the annotation: '''Flag=!ExcludedFromPool'''.
 4. Add all parent RNA items to the '''Flagged RNA''' biomaterial list.
 5. Check that the selection list in the '''Create pooled libraries''' no longer include already registered library plates.

=== 3. Fix !PoolConc values for all *.dil extracts ===

Due to a bug (see #507), all `*.dil` extracts have been registered with an incorrect value for the '''!PoolConc''' annotation. This need to be fixed by a manual export/import procedure.

 1. To find the libraries in question go to the '''Biomaterial LIMS->Extracts''' page and filter on '''name=%.dil'''. 
 2. To avoid rounding errors in the exported data go to '''BASE->Preferences''' and set '''Decimals=all'''.
 3. Use the '''Table exporter''' plug-in to export a tab-separated file with '''Name''' and '''Original quantity''' columns.
 4. Download the exported file to your computer and open in a spreadsheet program.
 5. Add a new column '''!PoolConc''' and use the following formula to calculate the values: `=5 * <quantity> / 1000`
 6. Save the results as a tab-separated file and upload it to BASE.
 7. Use the annotation importer to update the '''!PoolConc''' values.