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Create a pipeline

How to create a new pipeline?

A pipeline defines the processing steps for raw data files. Each pipeline belongs to a project and can be configured with specific parameters and input files for Maxquant and RawTools. To add a new pipeline, you need to have at least one project set up in the system. If you haven't created a project yet, please refer to Create a project before proceeding.

Click on the + Add button beside Pipelines to open the pipeline creation form:

Fill in the editable fields and upload the required configuration:

  1. Select the MaxQuant version. If no explicit version is selected, the default bundled version (2.4.12.0) is used.
  2. Add a FASTA file with the target protein sequences.
  3. Add an mqpar.xml file generated with MaxQuant. If no explicit mqpar.xml is submitted, the default mqpar.xml file for bundled version (2.4.12.0) is used. For template requirements such as the single-RAW assumption and placeholder handling, see How to prepare mqpar.xml.
  4. Provide command-line parameters for RawTools. Read RawTools help for the supported arguments.

Using a different MaxQuant version

The pipeline form only lets you choose from MaxQuant executables that are already installed on the server. The bundled 2.4.12.0 version is available automatically, but any other version must be added first by a server operator.

LAMPrEY scans the compute storage root recursively for files matching:

  • *MaxQuantCmd.exe
  • *MaxQuantCmd.dll

In the standard containerized deployment, that means the executable must live somewhere under:

  • /compute/

In the default local development setup from .env, that maps to:

  • ./data/compute/

The recommended layout is:

/compute/software/MaxQuant/MaxQuant_v_<version>/MaxQuantCmd.exe

or for newer .NET builds:

/compute/software/MaxQuant/MaxQuant_v_<version>/bin/MaxQuantCmd.dll

Example of the default bundled version:

/compute/software/MaxQuant/MaxQuant_v_2.4.12.0/MaxQuantCmd.exe
/compute/software/MaxQuant/MaxQuant_v_2.4.12.0/bin/MaxQuantCmd.dll

Current behavior:

  1. Install or extract the desired MaxQuant release on the server so that its MaxQuantCmd.exe or MaxQuantCmd.dll exists somewhere under /compute/ (or ./data/compute/ in a local non-container setup).
  2. Re-open the pipeline form. The executable should now appear in the MaxQuant version dropdown.
  3. Select that version and upload an mqpar.xml generated with the same MaxQuant release.

If the version does not appear in the dropdown, it is not installed in a location LAMPrEY scans yet.

For runtime details, see MaxQuant: versions earlier than 2.6 run through mono, while versions 2.6 and newer run through dotnet.

After saving the pipeline:

  • project members can upload .raw files to it from the pipeline page or via the API
  • each uploaded file creates an independent run, even when the displayed filename matches a previous upload
  • the seeded demo pipeline is read-only and blocks new uploads