Re: [galaxy-dev] [galaxy-bugs] Sequence Read Archive (SRA)
On Fri, Oct 08, 2010 at 01:40:01PM -0700, Shaun Jackman wrote:
Could the Sequence Read Archive (SRA) be added to the list of data sources?
To do this we need some way to communicate with the datasource, either some Galaxy awareness in the web site, or a reasonable API we can query data with, preferably both. Does anybody know what sort of API is avaialble for SRA?
On Fri, 2010-10-08 at 14:18 -0700, James Taylor wrote:
On Fri, Oct 08, 2010 at 01:40:01PM -0700, Shaun Jackman wrote:
Could the Sequence Read Archive (SRA) be added to the list of data sources?
To do this we need some way to communicate with the datasource, either some Galaxy awareness in the web site, or a reasonable API we can query data with, preferably both. Does anybody know what sort of API is avaialble for SRA?
Hi James, NCBI provides the SRA Software Development Kit: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software http://www.ncbi.nlm.nih.gov/Traces/sra/static/SRAToolkit.pdf Something as simple however as the user providing the SRP/SRX/SRR accession number and Galaxy downloading the data from NCBI's FTP site would be enough for me: ftp://ftp.ncbi.nlm.nih.gov/sra/ Cheers, Shaun
participants (2)
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James Taylor -
Shaun Jackman