Home

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:

• You have installed a Windows with .Net Framework 4.7.2 or above.

And that's all.

Installation

• Just download the last .zip release at this link https://github.com/proteomicsunitcrg/rawocop/releases and uncompress it in a folder.
• Place the uncompressed folder at some easily accessible location, e.g. the Desktop.
• Double click rawocop.exe file.

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.
    

• 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.

• 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:

• 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).

Rawocop + QSample

You can also install the rawocop alongside the QSample to send your RAW files to the pipeline. For this:

1. In your queue manager (typically Thermo Tune software), add a fourth column that will include the name of the database associated with the sample organism. The name should be exactly the same as 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 Tune software "SP_Human". [pending screenshots of Thermo Tune].
2. Install and configure the rawocop in your preferred Windows computer.
3. Make sure to configure the rawocop "Move files from" where the QSample RAW files are stored.
4. Enable the "Append database to QSample" checkbox.
5. Operate the rawocop as described in this documentation.