Changes between Version 4 and Version 5 of net.sf.basedb.reggie/notes427
- Timestamp:
- May 18, 2020, 11:50:38 AM (4 years ago)
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net.sf.basedb.reggie/notes427
v4 v5 5 5 == A. Before updating Reggie == 6 6 7 === 1. Install new/updated pipeline scripts ===7 === 1. Install updated pipeline scripts === 8 8 9 9 There are new pipeline scripts: http://baseplugins.thep.lu.se/browser/other/pipeline/trunk … … 12 12 * `novaseq_status.sh`: Used by auto-confirmation to check status of !NovaSeq sequencing. 13 13 14 === 2. Install R-script for the Single Sample Predictor ===14 === 2. Install R-script for the Single Sample Predictor (SSP) === 15 15 16 TODO 16 A 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 18 Extract this zip-file to a suitable location. Make sure that the files are accessible for the Tomcat user acccount. 19 17 20 18 21 === 3. Import annotation types that are required for storing SSP results === … … 25 28 == B. Update Reggie == 26 29 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. 30 Update Reggie to version 4.27. Some changes are required for `reggie-config.xml`: 31 32 The `<rscript>/<ssp>/<path>` entry should be modified to point to the **directory** where the R scripts are 33 installed (see step 2). 34 35 Add the following models to the `<rscript>/<ssp>/<models>` section 36 (remove the `<model>` entry that is already there). 29 37 30 38 {{{ … … 54 62 </model> 55 63 }}} 56 64 65 Do not forget to run the Installation wizard. 66 57 67 == C. Run SSP for existing !StringTie raw bioassays == 58 68