| | 1 | = Updating to Reggie 4.11 = |
| | 2 | |
| | 3 | === New pipeline for secondary analysis === |
| | 4 | |
| | 5 | '''Do not update to Reggie 4.11 if there are existing secondary analysis jobs running!! ''' |
| | 6 | |
| | 7 | The Tophat alignment and Cufflinks feature extraction parts of the secondary analysis has been merged to run as a single job (see #982 and #983). The new auto-confirm implementation can no longer handle the old type of jobs. There is also no interface for manually confirming or re-starting the old jobs. |
| | 8 | |
| | 9 | === New folder structure for the !ProjectArchive (see #981)=== |
| | 10 | |
| | 11 | When storing files for new items in the project archive, the site prefix (eg. 11, 22, etc.) is used for top-level folders. The site folders will be created automatically when needed. It is possible to manually create the folders before or after updating. Symbolic links are supported. |
| | 12 | |
| | 13 | Existing files are not moved automatically but it is possible to do this manually (optional): |
| | 14 | |
| | 15 | 0. Make sure that no secondary analysis jobs are running. |
| | 16 | 1. Move the files on the file server to the new location. |
| | 17 | 2. Log in to BASE and update the `DataFilesFolder` for all `DerivedBioasay` and `RawBioAssay` items. This should be a fairly simple by exporting the `ID` and `DataFilesFolder` annotation. Use a favorite editor to change the annotation and then import the file with the `Annotation importer` plug-in. |
| | 18 | 3. Update the `URL` property for all file items that are referencing files in the project archive. Use the "Search" function to find all files and then export the `ID` and `URL`. Use any editor to update the `URL` and import the file with the `File importer` plug-in. Note that this plug-in expects a path by default so change the `Identification method` option to `Internal ID`. |
