= Updating to Reggie 4.0 =


== 1. Updating Reggie ==

'''Do not update to Reggie 4.0 while there are secondary analysis jobs running! '''
This may cause output data files to not be found or linked to the incorrect location.

 1. Extract the new `reggie.jar` file and put it in the usual location.
 2. Configure the location of the `<external-archive>` in `reggie-config.xml`.
 3. Log in to BASE and run the plug-in installation wizard.
 4. Run the Reggie -> Installation wizard.
 5. It will still complain about the `ExternalArchive` file server. Configure it so that it can access the location specified in `<external-archive>`.

== 2. Move secondary analysis data files that belong to external samples ==

 1. Log in to the file server containing secondary analysis data files.
 2. Move all data files belonging to external samples to the new location as configured in `<external-archive>'. Keep the sub-directory structure as it it.
 3. Log in to BASE.
 4. Move all directories inside `/home/SCANB/SecondayAnalysis` belonging to external samples to `/home/External/SecondaryAnalysis`. This should be relatively simple to do:
   * Select all directories that have names that are not `11`, `22`, etc. or `Stratagene`. 
   * Then, use the `Move -> To another directory` function to move all selected directories to `/home/External/SecondaryAnalysis`.
 5. Change the `FileServer` item on all files inside the `/home/External/SecondaryAnalysis` to `ExternalArchive`. This can be done editing each file item manually, but if there are a lot files it may be better to use a batch importer.
   * Log in to the file server
   * Cd to the `<external-archive>` folder
   * Type `find -type f > allfiles.txt`. This should create a file containing the filenames of all files inside the `<external-archive>`.
   * Open this file in a text editor on your computer
   * Add a header line: `Path`
   * Replace the starting `./` on all lines with `/home/External/SecondaryAnalysis/`.
   * Upload the file to BASE
   * Start the file batch importer plug-in and import the uploaded file. Most parameter can be left at default values, except for those listed below:
   * Let the importer run. It should update a lot of files, but also skip some since not all files have been mapped to BASE.

|| '''Mode''' || update ||
|| '''Identification method''' || Path ||
|| '''Data header''' || Path ||
|| '''Complex column mappings''' || allow ||
|| '''Path''' || \Path\ ||
|| '''File server''' || !ExternalArchive ||
|| '''Item not found || skip ||