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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

warning So when you plan the queue, you must fill in the "Database" column database_column 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

warning You must also put your sample filename filename_short according the request to which it belongs. For instance, 2023MQ001_sample1. Do not use any character different from underscore "_" in the filename.

  1. Install and configure the rawocop in your preferred Windows computer. Make sure to configure the rawocop "Backup" folder backup_folder in the incoming_folder of the bioinformatics pipeline. Also remember to check the "Append database to QSample" checkbox append_checked .
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