ThermoRawFileParser for macOS (Apple silicon)

[wenbostar]

Does ThermoRawFileParser (ThermoRawFileParser-v.2.0.0-dev-osx-arm64.zip) work on macOS (Apple silicon)?

Below is the error encountered when running it on an Apple Silicon computer:

osx-arm64/ThermoRawFileParser -i=/home/test/test.raw -b=/home/test/test.mzML -f=2
[error] ThermoRawFileParser failed to convert test.raw (exit 137).

[caetera]

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/*

[YuanyeChi]

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

[caetera]

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.

[YuanyeChi]

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.

[caetera]

Thank you. I will include your workaround in the documentation.

[wenbostar]

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.

[caetera]

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?