| | 1 | = Updating to Reggie 4.0 = |
| | 2 | |
| | 3 | |
| | 4 | == 1. Updating Reggie == |
| | 5 | |
| | 6 | '''Do not update to Reggie 4.0 while there are secondary analysis jobs running! ''' |
| | 7 | This may cause output data files to not be found or linked to the incorrect location. |
| | 8 | |
| | 9 | 1. Extract the new `reggie.jar` file and put it in the usual location. |
| | 10 | 2. Configure the location of the `<external-archive>` in `reggie-config.xml`. |
| | 11 | 3. Log in to BASE and run the plug-in installation wizard. |
| | 12 | 4. Run the Reggie -> Installation wizard. |
| | 13 | 5. It will still complain about the `ExternalArchive` file server. Configure it so that it can access the location specified in `<external-archive>`. |
| | 14 | |
| | 15 | == 2. Move secondary analysis data files that belong to external samples == |
| | 16 | |
| | 17 | 1. Log in to the file server containing secondary analysis data files. |
| | 18 | 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. |
| | 19 | 3. Log in to BASE. |
| | 20 | 4. Move all directories inside `/home/SCANB/SecondayAnalysis` belonging to external samples to `/home/External/SecondaryAnalysis`. This should be relatively simple to do: |
| | 21 | * Select all directories that have names that are not `11`, `22`, etc. or `Stratagene`. |
| | 22 | * Then, use the `Move -> To another directory` function to move all selected directories to `/home/External/SecondaryAnalysis`. |
| | 23 | 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. |
| | 24 | * Log in to the file server |
| | 25 | * Cd to the `<external-archive>` folder |
| | 26 | * Type `find -type f > allfiles.txt`. This should create a file containing the filenames of all files inside the `<external-archive>`. |
| | 27 | * Open this file in a text editor on your computer |
| | 28 | * Add a header line: `Path` |
| | 29 | * Replace the starting `./` on all lines with `/home/External/SecondaryAnalysis/`. |
| | 30 | * Upload the file to BASE |
| | 31 | * 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: |
| | 32 | * Let the importer run. It should update a lot of files, but also skip some since not all files have been mapped to BASE. |
| | 33 | |
| | 34 | || '''Mode''' || update || |
| | 35 | || '''Identification method''' || Path || |
| | 36 | || '''Data header''' || Path || |
| | 37 | || '''Complex column mappings''' || allow || |
| | 38 | || '''Path''' || \Path\ || |
| | 39 | || '''File server''' || !ExternalArchive || |
| | 40 | || '''Item not found || skip || |
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