"sra-tools" needs interactive configuration

bioconda / bioconda-recipes

Conda recipes for the bioconda channel.

https://bioconda.github.io

MIT License

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"sra-tools" needs interactive configuration #33998

Open SilasK opened 2 years ago

SilasK commented 2 years ago

NCBI doesn't make our lives easy. They want to make an interactive configuration about the sratoolkit

package: "sra-tools"

This sra toolkit installation has not been configured.
Before continuing, please run: vdb-config --interactive
For more information, see https://www.ncbi.nlm.nih.gov/sra/docs/sra-cloud/

SilasK commented 2 years ago

Luckily there is an option --quiet

Should it be part of the bioconda package? e.g. a post script?

audy commented 2 years ago

I've bumped into this before. The solution was to create the file /.ncbi/user-settings. This is the contents of the file I used. I'm not sure which fields are actually required to skip the prompt:

/LIBS/GUID = "<redacted>"
/config/default = "false"
/libs/cloud/accept_aws_charges = "false"
/libs/cloud/report_instance_identity = "true"
/repository/user/default-path = "/tmp"
/repository/user/main/public/root = "/tmp"
/repository/user/main/public/cache-disabled = "true"