Changes between Version 5 and Version 6 of net.sf.basedb.reggie/notes423


Ignore:
Timestamp:
Sep 4, 2019, 2:35:02 PM (15 months ago)
Author:
Nicklas Nordborg
Comment:

Added note about updating BASE and about the DNANormalization protocol

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  • net.sf.basedb.reggie/notes423

    v5 v6  
    2929    - `<align-hisat>/<mark-duplicates-options>`
    3030
     31== 3. Update BASE to BASE 3.15.2 ==
    3132
    32 == 3. Install Reggie 4.23 and run the installation wizard ==
     33This version is needed because it includes the **Tag batch item importer** that is needed in a later stop to import barcodes for the MIPs libraries.
    3334
     35== 4. Install Reggie 4.23 and run the installation wizard ==
    3436
    35 == 4. Set a value for the Pipeline annotation on existing items ==
     37== 5. Set a value for the Pipeline annotation on existing items ==
    3638
    3739Almost all existing items from **Library** and downstream must be given a value for the **Pipeline** annotation. The table below specifies the value
     
    4951|| Software || Demuxing, Merging ||  -  || RNAseq ||
    5052
    51 == 5. Other updates to existing items ==
     53== 6. Other updates to existing items ==
    5254
    5355Existing **Hardware** items of type=**Sequencer** should be updated with a value for the **!FlowCellType** annotation. It should be either !NextSeq or !HiSeq.
    5456
    55 == 6. New items that should be created ==
     57== 7. New items that should be created ==
    5658
    5759|| **Item type** || **Subtypes** || **Additional settings** || **Comment** ||
    58 || Protocol || DNANormalization || !TargetAmount, !TargetMinimalAmount, !TargetVolume, MIPS_Pool || The protocol to use for normalizing DNA that should go into the MIPs pipeline. ||
     60|| Protocol || DNANormalization || !TargetAmount, !TargetMinimalAmount, !TargetVolume, MIPS_Pool || The protocol to use for normalizing DNA that should go into the MIPs pipeline. If no protocol exists, the option to pre-normalize DNA items (in the DNA/RNA/FlowThrough registration wizard) will not be enabled by default. Thus, it is recommended that a `DNANormalization` protocol is created only when needed. ||
    5961|| Protocol || Library preparation || !LibPrepTarget=MIPs || One or more protocols that will appear in the "MIPs library registration" wizard ||
    6062|| Protocol || Pooling || !LibPrepTarget=MIPs || One or more protocols that will appear in the MIPs pooling wizard ||
     
    6466|| Software || Merging || Pipeline=MIPs || One or more software entries that will appear in the MIPs demux wizard (merge section) ||
    6567
    66 == 7. Barcodes and barcode template plates ==
     68
     69== 8. Barcodes and barcode template plates ==
    6770
    6871Most of the barcode information (such as the sequences, positions, etc.) should be available as a file that can be used with batch importers. Some steps need to be done manually.
     
    9093
    9194
    92 == 8. User accounts for MIPs pipeline ==
     95== 9. User accounts for MIPs pipeline ==
    9396
    9497A user account that should work with the MIPs pipeline need to have the following group/role memberships: