ThermoRawFileParser for macOS (Apple silicon) #209

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1. caetera commented on Jul 2, 2026

   

   caetera

   on Jul 2, 2026

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   Hi @wenbostar,

   the support for Apple Silicon is still experimental (see #205, #202), since we currently lack a way to perform thorough testing on this platform. Judging by the error message it is not generated by TRFP, probably, it comes from a platform-specific wrapper. Can it be because of quarantine (as described in #202)?

   > xattr -dr com.apple.quarantine ThermoRawFileParser-v.2.0.0-dev-osx-arm64
   > xattr ThermoRawFileParser-v.2.0.0-dev-osx-arm64/*
   

   👍React with 👍1Reacted by Yuanye Chi
2. YuanyeChi commented on Jul 8, 2026

   

   YuanyeChi

   on Jul 8, 2026

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   Hi @wenbostar,

   the support for Apple Silicon is still experimental (see #205, #202), since we currently lack a way to perform thorough testing on this platform. Judging by the error message it is not generated by TRFP, probably, it comes from a platform-specific wrapper. Can it be because of quarantine (as described in #202)?

   > xattr -dr com.apple.quarantine ThermoRawFileParser-v.2.0.0-dev-osx-arm64
   > xattr ThermoRawFileParser-v.2.0.0-dev-osx-arm64/*
   

   Hi @caetera, thank you so much for providing the quarantine solution. I tried it and found that it did not completely solve the problem on my machine (macOS 15.7.4, M4 chip). I also needed to sign the executable after removing quarantine from the folder. Here is what I did FYI:

   1. Download the release from https://github.com/CompOmics/ThermoRawFileParser/releases/download/v.2.0.0-dev/ThermoRawFileParser-v.2.0.0-dev-osx-arm64.zip and extract it.

   2. In the parent folder, run:

   xattr -dr com.apple.quarantine ThermoRawFileParser-v.2.0.0-dev-osx-arm64
   xattr ThermoRawFileParser-v.2.0.0-dev-osx-arm64/*
   
   cd ThermoRawFileParser-v.2.0.0-dev-osx-arm64
   
   chmod +x ThermoRawFileParser
   
   # This is important because the dev build seems unable to pass Apple's security check without signing.
   codesign --force --deep --sign - ./ThermoRawFileParser

   👍React with 👍1Reacted by Bo
3. caetera commented on Jul 8, 2026

   

   caetera

   on Jul 8, 2026

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   Hi @YuanyeChi ,
   thank you for sharing this information. Since I have a little experience with Apple platform could you, please, clarify for me if the last signing step can be performed by any user or it requires some special permission, for example, a developer account.
4. YuanyeChi commented on Jul 8, 2026

   

   YuanyeChi

   on Jul 8, 2026

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   Hi @YuanyeChi , thank you for sharing this information. Since I have a little experience with Apple platform could you, please, clarify for me if the last signing step can be performed by any user or it requires some special permission, for example, a developer account.

   No problem. I don’t think I have a developer account to sign this. With this codesign command, I think I only made the ThermoRawFileParser executable work locally on my machine after removing the quarantine attribute. I am guessing that a developer account is still needed if this is intended to be used by other Mac users.

   👍React with 👍1Reacted by Vladimir Gorshkov
5. caetera commented on Jul 8, 2026

   

   caetera

   on Jul 8, 2026

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   Thank you. I will include your workaround in the documentation.
6. wenbostar commented on Jul 8, 2026

   

   wenbostar

   on Jul 8, 2026

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   Hi @caetera , will it be possible to make it work without these additional process? This will be very useful for some automatic pipelines which call TRFP for data conversion.
7. caetera commented on Jul 17, 2026

   

   caetera

   on Jul 17, 2026

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   Hi @wenbostar,

   after a brief investigation, it seems like the only option to completely avoid any Gatekeeper warnings on Mac is to obtain a developer ID for 100$/year and sign/notarize the app through Apple. I am not sure if we have a budget for that.
   @ypriverol do you know anything about it?
8. mansanlab commented on Oct 9, 2026

   

   mansanlab

   on Oct 9, 2026

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   Hey @caetera, sorry for SUCH a delayed response dating all the way back to #202 and #205.

   I think I have a solution that works natively on Apple Silicon using the newest CommonCore dll's published by Thermo and without by passing any MacOS permissions/security features. In theory this should work for any platform, given all dependencies are built for AnyCPU, which I think only mzLib remains to be built for AnyCPU, but this worked regardless.

   0. Install dotnet@8

   >>> brew install dotnet@8
   

   1. Get the two repos in one directory

   >>> mkdir trfp-anycpu
   >>> cd trfp-anycpu
   >>> git clone https://github.com/compomics/ThermoRawFileParser.git  
   >>> git clone --depth 1 https://github.com/thermofisherlsms/RawFileReader.git
   >>> cd ThermoRawFileParser
   

   2. Change PlatformTarget and Platforms to "AnyCPU" within ThermoRawFileParser/ThermoRawFileParser.csproj and ThermoRawFileParser/ThermoRawFileParserTest/ThermoRawFileParserTest.csproj

   <PlatformTarget>x64</PlatformTarget> --> <PlatformTarget>AnyCPU</PlatformTarget>
   

   <Platforms>x64</Platforms> --> <Platforms>AnyCPU</Platforms>
   

   3. Update the ThermoFisher.CommonCore.RawFileReader version within ThermoRawFileParser/ThermoRawFileParser.csproj

   <PackageReference Include="ThermoFisher.CommonCore.RawFileReader" Version="8.0.6" /> --> <PackageReference Include="ThermoFisher.CommonCore.RawFileReader" Version="8.0.42" />
   

   As of 9 Oct 2026 this is version 8.0.42

   4. Link NuGet to Thermo's new packages

   >>> dotnet new nugetconfig
   >>> dotnet nuget add source  "../RawFileReader/Libs/NetCore/Net8" -n RawFileReader --configfile nuget.config
   

   5. Build

   >>> dotnet build ThermoRawFileParser.csproj -c Release
   

   6. Test

   >>> dotnet bin/Release/net8.0/ThermoRawFileParser.dll -i ThermoRawFileParserTest/Data/small.RAW -o . -f 2