Updating to Reggie 4.11

New pipeline for secondary analysis

Do not update to Reggie 4.11 if there are existing secondary analysis jobs running!!

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.

New folder structure for the ProjectArchive (see #981)

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.

Existing files are not moved automatically but it is possible to do this manually (optional):

0. Make sure that no secondary analysis jobs are running.
1. Move the files on the file server to the new location.
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.
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.