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anvilproject / anvil-docker

Docker containers for Anvil Project
MIT License
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gsutil requires CRC32c mod #25

Open mtmorgan opened 3 years ago

mtmorgan commented 3 years ago

Reported by a participant during a PopUp workshop

> avworkspace(thousand_genomes)
[1] “anvil-datastorage/1000G-high-coverage-2019”
> dir.create(“1000G”)
> avtable(“sample”) %>% pull(gVCF) %>% head(1) %>% gsutil_cp(destination = “~/1000G”)

results in

CommandException: Downloading this composite object requires integrity checking with CRC32c,
but your crcmod installation isn’t using t...

which I think is a gsutil configuration step that should be performed on the image. See gsutil help crcmod

rtitle commented 3 years ago

May need to do something similar to this in the RStudio image: https://github.com/DataBiosphere/terra-docker/blob/master/terra-jupyter-base/Dockerfile#L140

briandoconnor commented 3 years ago

@rtitle , do you know if this is being worked on across the various images (RStudio, Jupyter, etc?). It seems like every image launched by Terra for interactive analysis should just have this installed. I believe it's installed in the Cromwell images used for batch analysis.

rtitle commented 3 years ago

Yes, we have this ticket to replicated recent fixes (including crcmod) to the RStudio image: https://broadworkbench.atlassian.net/browse/IA-2771