Changes between Initial Version and Version 1 of net.sf.basedb.reggie/notes415


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Timestamp:
Jan 29, 2018, 2:36:19 PM (5 years ago)
Author:
Nicklas Nordborg
Comment:

Added update notes for Reggie 4.15

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  • net.sf.basedb.reggie/notes415

    v1 v1  
     1= Updating to Reggie 4.15 =
     2
     3=== New !StringTie pipeline in the Hisat secondary analysis ===
     4
     5In `reggie-config.xml` the following changes are required:
     6
     7 * In the `<programs>` section, a `<stringtie>` sub-section should be added with the full `<path>` to the !StringTie executable.
     8 * A `<stringtie>` section with !StringTie configuration parameters should be added. The configuration file shipped with Reggie should contain functional default values.
     9
     10=== New annotation on feature extraction software and protocols ===
     11
     12A new annotation type, `ExpressionType` has been added. Find existing software and protocols with `Type=Feature extraction` and set the `ExpressionType` annotation to `Cufflinks`.
     13
     14Create a new software and protocol item for the !StringTie pipeline. They should have `Type=Feature extraction` and `ExpressionType=StringTie`. Keep the `Add as project default` checkbox checked and the `Replace existing default` unchecked.