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ewels / sra-explorer

Web application to explore the Sequence Read Archive.
https://sra-explorer.info/
GNU General Public License v2.0
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Update SRA downloads #15

Open ewels opened 5 years ago

ewels commented 5 years ago

As reported in https://github.com/ewels/sra-explorer/issues/14 and mentioned in this blog post, the NCBI SRA will be retiring the FTP server that is currently linked to from sra-explorer.

This page has up to date information on how the SRA recommends that data is downloaded. Sounds like we should give commands for prefetch. We might also be able to guess the HTTPS URLs if they are as simple as the one in the example: https://sra-download.ncbi.nlm.nih.gov/srapub/SRR000001. Could then give raw HTTPS links and also aspera download commands.

ewels commented 5 years ago

..though they really want you to use prefetch.

ewels commented 3 years ago

The SRA on AWS s3 should now have paths that can be inferred! 🎉 

s3://sra-pub-run-odp/sra/accession/accessionfile

I think that we could now have download commands that look like this:

aws s3 sync s3://sra-pub-run-odp/sra/XXX/ . --include "XXX*"

The slightly odd command format is so that it downloads the .sra file but also the .vdbcache file if it exists.