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GEO downloader doesn't work due to NCBI API changes #54

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iromeo opened this issue Feb 28, 2018 · 0 comments
Open

GEO downloader doesn't work due to NCBI API changes #54

iromeo opened this issue Feb 28, 2018 · 0 comments
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@iromeo
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iromeo commented Feb 28, 2018

E.g. we cannot batch download files by GSMxxx id using GSMnnn to SRXnnn mapping and NCBI FTP /ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX . So we cannot use aspera or rsync with urls like rsync://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX212/SRX212665.

Alternative way is:

We need to change scripts/geo_rsync.sh to support that.

@iromeo iromeo self-assigned this Feb 28, 2018
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