Changes between Version 3 and Version 4 of net.sf.basedb.reggie.notes213


Ignore:
Timestamp:
Oct 2, 2013, 1:27:21 PM (6 years ago)
Author:
Nicklas Nordborg
Comment:

More instructions for the manual fix for #508

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  • net.sf.basedb.reggie.notes213

    v3 v4  
    11= Updating to Reggie 2.13 =
    22
    3 '''IMPORTANT! ''' Before installing this update, 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.
     3'''IMPORTANT! ''' Before installing this update, there are a number of things that need to be checked and manually fixed!!!
    44
    5 A manual update is needed to flag libraries and their parent RNA items which have 0 original quantity due to no value received from Qubit concentration measurement. More instructions will follow. For now see #508.
     5=== 1. Make sure that pools have been registered ===
    66
     7Make 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.
     8
     9=== 2. Flag some libraries and their parent RNA item ===
     10
     11Due 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.
     12
     13 1. To find the libraries in question go to the '''Biomaterial LIMS->Extracts''' page and filter on '''Type=Library''' and '''CA_Molarity=0'''.
     14 2. Edit each library item and set the annotation: '''Flag=!ExcludedFromPool'''.
     15 3. Find the parent RNA item for each library and set the annotation: '''Flag=!ExcludedFromPool'''.
     16 4. Add all parent RNA items to the '''Flagged RNA''' biomaterial list.
     17 5. Check that the selection list in the '''Create pooled libraries''' no longer include already registered library plates.
     18
     19=== 3. Fix !PoolConc values for all *.dil extracts ===
    720A manual update is needed to fix `PoolConc` values for existing `*.dil` extracts. More instructions will follow. For now, see #507.