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Roger Olivella edited this page Jan 27, 2023 · 47 revisions

Welcome to the rawocop wiki!

Requirements

rawocop works in a PC with Windows. Full stop. But if you unlikely have any issue with the installation you should check that:

And that's all.

Installation

Notes:

  • If your Windows version complains (especially Windows 10) that is an unrecognized program and potentially harmful, run it anyway.
  • If there's another rawocop.exe from a previous version, just delete it.

Configuration

  • Fill in the "Root folders location":

    • Click to "Input folder" and select the folder where the raw files are. Could be the "C:\XCalibur\data" folder, for instance.
    • Click to "Backup folder" and select the folder where you want to move your files. Could be the "C:\backup" folder, for instance.
      root2

  • Check/Uncheck "Enable backup folders" and/or Check/Uncheck "Discard QCloud files":

    • Click to "Enable backup folders" if you want to backup your files to a set of subfolders that is automatically created by reading the RAW files. For instance, you can configure rawocop to backup the files to "C:\backup\Instrument name\YYMM", where "Instrument name" could be "orbitrap_exploris" and "YYMM" the current year and month "2207". So the final folder where the RAW files will be moved is "C:\backup\orbitrap_exploris\2207".
    • Click to "Discard QCloud files" to DO NOT backup QCloud files, that is, files with "QC01" or "QC02" in its filename.
    • If you are using rawocop together with QSample, you must enable the "Append database to QSample". Please check this decicated documentation to install RAWocop alongside QSample. 2023-01-26 15_40_23-Window

  • Review "Summary". Check in this panel the original folder (where are the original RAW files) and where are they going to be copied.

    • For instance: summary

  • Finaly click at “START backuping!”. This means that the program will monitor new raw files at your local data folder and will move them automatically.

Important note: this program needs to be always running. If you reboot your computer please reload it.

Rawocop checks

Rawocop does not perform the backup if the RAW file:

  • Is in use or locked by another program (for instance, you have it opened in the XCalibur viewer or is in acquisition process).
  • Rawocop does not have permissions to create the backup folder.
  • Has no MS data.
  • Already exists in the backup folder.
  • Is very big (> 10 GB).
  • Is very small (< 10 MB).

Install rawocop alongside QSample

  1. In your queue manager (typically Thermo Scientific XCalibur), add a column that must include the name of the database associated with the sample organism. For this, click on the top menu option Change > Column arragement...

column_arrangement

And add a new column labeled as "Database":

Screenshot from 2023-01-27 12-12-26

So when you planify the queue, you must fill in the "Database" for the files you want to monitor within the QSample, with the name defined in the database folder of QSample. For instance, if the FASTA is in the folder /home/username/databases/SP_human/current/sp_human_04_2023.fasta, you'll put in the Thermo Scientific XCalibur software the "SP_Human":

xcalibur_hihglight

  1. Install and configure the rawocop in your preferred Windows computer. Make sure to configure the rawocop "Backup" folder where the QSample RAW files are stored. Also remember to check the "Append database to QSample" checkbox.
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