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Add way for users to specify API keys for NCBI #41

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zachary-foster opened this issue Dec 15, 2023 · 1 comment
Open

Add way for users to specify API keys for NCBI #41

zachary-foster opened this issue Dec 15, 2023 · 1 comment

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@zachary-foster
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This is needed to avoid downloading references to fail due to rate limits
@zachary-foster
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We communicate with NCBI in the following modules

  • SRATOOLS_FASTERQDUMP (using fasterq-dump)
  • DOWNLOAD_ASSEMBLIES (using datasets)
  • FIND_ASSEMBLIES (using entrez eutils)

It looks like only DOWNLOAD_ASSEMBLIES allows specifying the API key on the command line so we need to specify with an environmental variable in the others,

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