Changes between Version 4 and Version 5 of net.sf.basedb.reggie/notes427


Ignore:
Timestamp:
May 18, 2020, 11:50:38 AM (9 days ago)
Author:
Nicklas Nordborg
Comment:

Added instructions for installing SSP scripts and models

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  • net.sf.basedb.reggie/notes427

    v4 v5  
    55== A. Before updating Reggie ==
    66
    7 === 1. Install new/updated pipeline scripts ===
     7=== 1. Install updated pipeline scripts ===
    88
    99There are new pipeline scripts: http://baseplugins.thep.lu.se/browser/other/pipeline/trunk
     
    1212 * `novaseq_status.sh`: Used by auto-confirmation to check status of !NovaSeq sequencing.
    1313
    14 === 2. Install R-script for the Single Sample Predictor ===
     14=== 2. Install R-script for the Single Sample Predictor (SSP) ===
    1515
    16 TODO
     16A zip-file with all R script and model .RData files that are needed can be found at `casa4:/home/thep-nni/ssp/SSP.zip`.
     17
     18Extract this zip-file to a suitable location. Make sure that the files are accessible for the Tomcat user acccount.
     19
    1720
    1821=== 3. Import annotation types that are required for storing SSP results ===
     
    2528== B. Update Reggie ==
    2629
    27 Update Reggie to version 4.27. Add the following models to the `<rscript>/<ssp>/<models>` section
    28 in `reggie-config.xml` (remove the `<model>` entry that is already there). Do not forget to run the Installation wizard.
     30Update Reggie to version 4.27. Some changes are required for `reggie-config.xml`:
     31
     32The `<rscript>/<ssp>/<path>` entry should be modified to point to the **directory** where the R scripts are
     33installed (see step 2).
     34
     35Add the following models to the `<rscript>/<ssp>/<models>` section
     36(remove the `<model>` entry that is already there).
    2937
    3038{{{
     
    5462</model>
    5563}}}
    56  
     64
     65Do not forget to run the Installation wizard.
     66
    5767== C. Run SSP for existing !StringTie raw bioassays ==
    5868