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Installation Guide

System Requirements

  • Julia: 1.10 or higher
  • CPU: Multiple cores and threads recommended. Increasing the number of threads reduces computation time.
  • RAM: >=16GB recommended. RAM availability should exceed the spectral library size by at least 4GB. For searching against the yeast proteome, as little as 6-8 GB may suffice.
  • Storage: SSD recommended. Available disk space at least double the total size of the .arrow formmated raw files to search. The .arrow files are usually ~1/2 the size of the vendor files.
  • Operating System: Windows, Linux, or macOS

Installation Steps

1. Install Julia

  1. Download and install Julia 1.10 or higher from julia.org
  2. Verify installation by opening the Julia REPL and checking the version:
julia> versioninfo()
Julia Version 1.10.0
...

2. Install Pioneer.jl

Standard Instructions

  1. Start the Julia REPL and install 
julia> using Pioneer
[ Info: Precompiling Pioneer [585db54e-1982-41c9-ae07-9e9eb56c7d61]
┌ Info: Skipping precompilation due to precompilable error. Importing Pioneer [585db54e-1982-41c9-ae07-9e9eb56c7d61].
└ exception = Error when precompiling module, potentially caused by a __precompile__(false) declaration in the module.
  1. Test your installation. From the REPL, enter package mode (press ]), then:
(@v1.11) pkg> test Pioneer

Developeer Instructions

To install Pioneer for development, clone the github repository and use in a local environment according to these instructions.

  1. Open Command Prompt (Windows) or Terminal (MacOSX/Linux) and clone the repository:
    git clone https://github.com/nwamsley1/Pioneer.jl.git
cd Pioneer.jl
  2. Start Julia and enter package mode (press ]), then:
    pkg> activate .
pkg> develop ./
  3. Return from package mode (backspace) and verify installation:
    julia> using Pioneer
  4. Test your installation. Enter package mode (press ]), then:
    pkg> test
'note'

On the first attempt using Pioneer requires an internet connection, and it may take several minutes to download and install dependencies.

'note'

The best way to develop Pioneer is with the help of the Revise package.

3. Install PioneerConverter

Pioneer requires Thermo RAW files to be converted to Apache Arrow format. The cross-platform PioneerConverter package does the conversion.

  1. Download .NET 8.0 SDK and .NET Runtime 8.0 here

  2. Download and install PioneerConverter

    • Using Release (recommended):

    • Build locally:

      • Clone the repository git clone https://github.com/nwamsley1/PioneerConverter.git
      • Navitage inside of the PioneerConverter directory and run: dotnet build -c Release

  3. Test your installation:

    • Using the Command Prompt (windows) or Terminal (MaxOS/Linus), navigate inside of the PioneerConverter directory.
      • Windows: cmd bin\Release\net8.0\PioneerConverter.exe \path\to\test\raw\file.raw -b 10000
      • Linux/macOS: bin/Release/net8.0/PioneerConverter /path/to/test/raw/file.raw -b 10000
'note'

Pioneer.jl has experimental support for converting .mzML formatted SCIEX TOF data to the .arrow format via the convertMzML method.

Next Steps

After installation:

  1. Follow the Quick Start Tutorial
  2. Review Parameter Configuration