Changes between Version 1 and Version 2 of net.sf.basedb.relax/notes14

Jan 17, 2019, 11:26:05 AM (5 years ago)
Nicklas Nordborg

Added update note for Relax 1.4 related to Cufflinks and StringTie annotation categories


  • net.sf.basedb.relax/notes14

    v1 v2  
    11= Updating to Relax 1.4 =
    3 The following steps should be done after installing Relax 1.4
     3The following steps should be done after installing Relax 1.4.
    55=== Create Lysate items between RNA and Specimen ===
    99The '''Relax installation wizard''' contains a function for doing this. When you enter the installation wizard it will most likely complain about some missing subtypes and annotation type, etc. After fixing this the installation wizard should display a note about the number of `RNA` items that are linked to `Specimen` items and a button '''Create Lysate and re-link RNA'''. Click on this button and wait for the installation wizard to finish. It will take some time for it to finish but it will save the results at regular intervals so if there is a problem it should be possible to re-start and try again.
     11=== Add annotation types to the Cufflinks and !StringTie categories ===
     13The Cohort exporter and Level 3 exporter plug-ins has been updated to only export annotations and data that is correctly shared and matched against raw data types (#1099). To make sure that the proper annotations are included when exporting the following steps need to be done:
     15Go to the '''Administrate - Types - Annotation type categories''' page and locate the `Cufflinks` and `StringTie` categories. Open the edit dialog for each one, switch to the '''Annotation types''' tab. The only annotation type so far should be the `FirstReleasedIn` annotation type. Add more annotation types:
     17 * For `Cufflinks`: All annotation types for raw bioassays except the `QC_GenoTypeHET_PCT` annotation.
     18 * For `StringTie`: All annotation types for raw bioassays except those starting with `PILOT_`.
     20The categories also need to be shared to the releases (=projects) that they are used in. For the `Cufflinks` category this typically means that it should be shared with READ permission to all existing projects and for the `StringTie` category that is should be shared to the 4.0 project.