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nextstrain / nextclade

Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
https://clades.nextstrain.org
MIT License
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Dataset download not working #1083

Closed denise0593 closed 1 year ago

denise0593 commented 1 year ago

Dear team, I'm trying to download the human MonkeyPox reference, I've tried to download it with the following command line, but nothing happened. docker run -it --rm nextstrain/nextclade:latest nextclade dataset get --name 'hMPXV' --reference 'NC_063383.1' --output-dir data/human_monkey

What I'm doing wrong? Thanks a lot

fanninpm commented 1 year ago

Did you mount a volume when you invoked the docker run command?

docker run -it --rm -u $(id -u):$(id -g) -v /path/to/local/directory:/data nextstrain/nextclade:latest nextclade dataset get --name 'hMPXV' --reference 'NC_063383.1' --output-dir data/human_monkey
ivan-aksamentov commented 1 year ago

@denise0593 What are you expecting to happen? You are downloading a dataset into the container filesystem. If you want it on your host machine, mounting a volume and setting output dir to that volume as @fanninpm mentioned should help. This does not seem to be an issue in Nextclade. But if you think there is, feel free to comment and/or ope a new issue.