[BUG] cannot download a single experiment from command line

saketkc / pysradb

Package for fetching metadata and downloading data from SRA/ENA/GEO

https://saketkc.github.io/pysradb

BSD 3-Clause "New" or "Revised" License

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[BUG] cannot download a single experiment from command line #201

Open marcomoretto opened 10 months ago

marcomoretto commented 10 months ago

Describe the bug Running pysradb from command line to download a single experiment SRX results into the program hanging forever.

To Reproduce Steps to reproduce the behavior: pip install git+https://github.com/saketkc/pysradb pysradb download -y -t 8 --out-dir ./pysradb_downloads -x SRX1254413

Additional context I used Google colab to reproduce the bug with the latest version of pysradb available in GitHub

saketkc commented 8 months ago

Thanks for catching this and apoligies for the delayed response. I think there is a bug in the download module. For now I would recommend saving the metadata in a csv using pysradb metadata --detailed <SRP> --saveto x.tsv and using a tool like curl/wget to download files from the *_url column