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

Timestamp:

May 18, 2020, 11:50:38 AM (4 years ago)

Author:

Nicklas Nordborg

Comment:

Added instructions for installing SSP scripts and models

net.sf.basedb.reggie/notes427

@@ -5 +5 @@
 == A. Before updating Reggie ==
 
-=== 1. Install new/updated pipeline scripts ===
+=== 1. Install updated pipeline scripts ===
 
 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.
 
-=== 2. Install R-script for the Single Sample Predictor ===
+=== 2. Install R-script for the Single Sample Predictor (SSP) ===
 
-TODO
+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`. 
+
+Extract this zip-file to a suitable location. Make sure that the files are accessible for the Tomcat user acccount.
+
 
 === 3. Import annotation types that are required for storing SSP results ===
@@ -25 +28 @@
 == B. Update Reggie ==
 
-Update Reggie to version 4.27. Add the following models to the `<rscript>/<ssp>/<models>` section 
-in `reggie-config.xml` (remove the `<model>` entry that is already there). Do not forget to run the Installation wizard.
+Update Reggie to version 4.27. Some changes are required for `reggie-config.xml`:
+
+The `<rscript>/<ssp>/<path>` entry should be modified to point to the **directory** where the R scripts are
+installed (see step 2).
+
+Add the following models to the `<rscript>/<ssp>/<models>` section 
+(remove the `<model>` entry that is already there).
 
 {{{
@@ -54 +62 @@
 </model>
 }}}
- 
+
+Do not forget to run the Installation wizard.
+
 == C. Run SSP for existing !StringTie raw bioassays ==