Changes between Initial Version and Version 1 of net.sf.basedb.reggie/notes40


Ignore:
Timestamp:
Nov 13, 2015, 2:00:43 PM (5 years ago)
Author:
Nicklas Nordborg
Comment:

First version of update notes for Reggie 4.0 (moving external files to new location)

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  • net.sf.basedb.reggie/notes40

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     1= Updating to Reggie 4.0 =
     2
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     4== 1. Updating Reggie ==
     5
     6'''Do not update to Reggie 4.0 while there are secondary analysis jobs running! '''
     7This 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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