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Load FASTQ from HTTP, FTP, and SRA/similar #1

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niemasd opened this issue Sep 28, 2023 · 3 comments
Open

Load FASTQ from HTTP, FTP, and SRA/similar #1

niemasd opened this issue Sep 28, 2023 · 3 comments
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enhancement New feature or request

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@niemasd
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niemasd commented Sep 28, 2023

@daniel-ji @robertaboukhalil In the future, it might be nice to add functionality to be able to load a FASTQ from HTTP and FTP (using wget to download it) as well as SRA/similar (using whatever the current best way of downloading FASTQs from SRA currently is).

The use case I'm imagining is that one of my collaborators sent me the URL of a FASTQ she had already analyzed but wanted to rerun using ViralConsensus to get the position base counts to see how well-supported each position is, and I had to run everything for her because of the need to install tools, whereas if the ViralWasm-Consensus web app had the ability to download a FASTQ from a URL, she could have easily rerun everything herself much faster (due to overhead of me checking my email, getting to my computer, downloading the files, rerunning when I had time, sending back, her checking her email, etc.) because of the simple point-and-click no-install environment

Let's keep this as a low priority that we can incorporate in the future (definitely after we submit the paper for review; so benchmarking should be the main priority), but it might be nice to have

@niemasd
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niemasd commented Sep 28, 2023

In hindsight, I guess my collaborator could have just downloaded the file via HTTP from her web browser and then run ViralWasm-Consensus as it currently functions on the local downloaded version of the file, so maybe HTTP/FTP are even less urgent (though would be nice to have). So this feature even lower on the priority list

@daniel-ji
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Sounds good, noted!

@robertaboukhalil
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For future reference, with Aioli, you can mount a URL to the virtual file system to satisfy this use case. Caveats: the URL must have the right CORS settings for this to work without a server, and FTP is not supported in browsers.

@niemasd niemasd added the enhancement New feature or request label Oct 3, 2023
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