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sirius-ms / sirius

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)
GNU Affero General Public License v3.0
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Running Sirius 4.8.2 through Qemistree #38

Closed bsedio closed 2 years ago

bsedio commented 3 years ago

I am trying to run the latest version of Sirius (4.8.2), instead of 4.0.1, but although I've downloaded the newest version, the files are structured differently and I don't know how to reference the bin folder.

The Qemistree tutorial is set up like this;

qiime qemistree predict-fingerprints --p-sirius-path '/Users/briansedio/Documents/Sirius/sirius-osx64-4.0.1/bin' \ --i-molecular-formulas molecular_formulas.qza \ --p-ppm-max 20 \ --p-java-flags "-Djava.io.tmpdir=/Users/briansedio/Documents/QemUT/demo-qemistree/javatemp -Xms16G -Xmx64G" \ --o-predicted-fingerprints fingerprints.qza

But for the Sirius 4.8.2, there is no Sirius/sirius-version/bin folder. Would you know how to modify that line to run Sirius 4.8.2 correctly?

Thank you very much, Brian

marcus-ludwig commented 2 years ago

Dear Brian,

I hope you could already resolve your issue. Still, here's a late response: I am assuming you are using the macOS version. This should contain a directory sirus-gui.app/Contents/MacOS that contains the executables. I hope this helps.

Please note that the current SIRIUS version is 4.9.5 and 5.0 will be coming soon with great new features.

Best, Marcus