Changes between Version 4 and Version 5 of net.sf.basedb.reggie/notes423


Ignore:
Timestamp:
Sep 4, 2019, 8:58:07 AM (13 months ago)
Author:
Nicklas Nordborg
Comment:

More update instructions

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  • net.sf.basedb.reggie/notes423

    v4 v5  
    11= Updating to Reggie 4.23 =
    22
    3 TODO - when to do the different steps!
     3----
     4**IMPORTANT! ** \\
     5This update requires a lot of manual work to install. Some things should be prepared in advance and some things should be
     6done after Reggie 4.23 has been installed. Make sure to assign enough time for the update. No-one should be working with
     7registrations and other things during the upgrade since some wizards may not work correctly until the update has been completed.
     8It is also important to no secondary analysis jobs are running, since this may cause the results to be incorrectly registered
     9or not registered at all.
     10----
    411
    5 TODO - state requirements: no current sequencing or secondary analysis jobs
     12== 1. New pipeline scripts ==
    613
    7 == 1. Set value for Pipeline annotation on existing items ==
     14There are new pipeline scripts: http://baseplugins.thep.lu.se/browser/other/pipeline/trunk
     15Download and install at a suitable location on the prime cluster.
    816
    9 Almost all existing items from Library and downstream must be given a value for the **Pipeline** annotation. The table below specifies the value
     17== 2. Changes in reggie-config.xml ==
     18
     19There are several changes in reggie-config.xml:
     20
     21 * The path to the pipeline scripts must be changed to point to the new version.
     22 * The path to Picard must be changed to a newer version: `/usr/local/packages/picard-tools/2.20.0`.
     23 * A new section for the MIPs demux has been added `<demux-mips>`. The default parameters can probably be used.
     24 * The parameter syntax for Picard has been changed. The old syntax `key=value` has been changed to `-key value`. This affects several
     25   existing configuration settings:
     26    - `<demux>/<extract-options>`
     27    - `<demux>/<fastq-options>`
     28    - `<align>/<mark-duplicates-options>`
     29    - `<align-hisat>/<mark-duplicates-options>`
     30
     31
     32== 3. Install Reggie 4.23 and run the installation wizard ==
     33
     34
     35== 4. Set a value for the Pipeline annotation on existing items ==
     36
     37Almost all existing items from **Library** and downstream must be given a value for the **Pipeline** annotation. The table below specifies the value
    1038to set for the Pipeline annotation for different types of items. It should be possible to do a manual batch export/import for each row or groups of rows.
    1139
     
    2149|| Software || Demuxing, Merging ||  -  || RNAseq ||
    2250
    23 == 2. Other updates to existing items ==
     51== 5. Other updates to existing items ==
    2452
    25 Existing Hardware items of type=Sequencer should be updated with a value for the **!FlowCellType** annotation. It should be either !NextSeq or !HiSeq.
     53Existing **Hardware** items of type=**Sequencer** should be updated with a value for the **!FlowCellType** annotation. It should be either !NextSeq or !HiSeq.
    2654
    27 == 3. New items that should be created ==
     55== 6. New items that should be created ==
    2856
    2957|| **Item type** || **Subtypes** || **Additional settings** || **Comment** ||
     
    3664|| Software || Merging || Pipeline=MIPs || One or more software entries that will appear in the MIPs demux wizard (merge section) ||
    3765
    38 == 4. Barcode templates ==
     66== 7. Barcodes and barcode template plates ==
    3967
    4068Most 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.
    4169
    42  1. A barcode templates is represented as a **Bioplate** item where each coordinate is linked to a **Tag** item. Start by manually creating the required number of bioplates. They should have the following values:
    43 
    44 || **Bioplate type** || !BarcodeTemplate ||
    45 || **Plate geometry** || 96-well (8x12) ||
    46 || **Pipeline** (annotation) || MIPs ||
    47 
    48 
    49  2. Import/create **Tag** items from file using the batch **Tag importer** and then add annotations with the **Annotation importer**. The following values are required:
     70 1. Import/create **Tag** items from file using the batch **Tag importer** and then add annotations with the **Annotation importer**. The following values are required:
    5071
    5172|| **Name** || Name of the barcode/tag which must be unique ||
     
    5374|| **!BarcodeSequence** || The barcode sequence for the first index read ||
    5475|| **BarcodeSequence2** || The barcode sequence for the second index read ||
     76
     77 2. A barcode template is represented as a **Bioplate** item where each coordinate is linked to a **Tag** item. Start by manually creating the required number of bioplates. They should have the following values:
     78
     79|| **Bioplate type** || !BarcodeTemplate ||
     80|| **Plate geometry** || 96-well (8x12) ||
     81|| **Pipeline** (annotation) || MIPs ||
    5582
    5683 3.  Link the barcodes to templates. This is done by creating (virtual) extracts and link them with tags and positions on one of the bioplates created in the first step. It should be possible to do this with the batch **Extract importer**:
     
    6188|| **Biowell row** || Row coordinate on the template bioplate (A-H) ||
    6289|| **Biowell column || Column coordinate on the template bioplate (1-12) ||
     90
     91
     92== 8. User accounts for MIPs pipeline ==
     93
     94A user account that should work with the MIPs pipeline need to have the following group/role memberships:
     95
     96 * Groups: `SCAN-B Lab`, `MIPsSecondaryAnalysis`
     97 * Roles: `User`, `MIPsLibraryPrep`, `MIPsPlateDesigner`
     98