anton wrote, On 04/01/2011 09:02 PM:
We are getting multiple requests for this but did not have the bandwidth to do it. So if you are planning to implement - share through the toolshed and we will roll it to main.
To start, this patch adds "SRA" binary type with sniffing and upload support: http://cancan.cshl.edu/labmembers/gordon/files/sra_binary_data_type.patch It only adds the datatype to "datatypes_conf.xml.sample", so existing installations must manually add the following lines to their ""datatypes_conf.xml": <datatype extension="sra" type="galaxy.datatypes.binary:Sra" mimetype="application/octet-stream" display_in_upload="true"/> and <sniffer type="galaxy.datatypes.binary:Sra"/> A question to people who are using "fastq-dump" on the command line: What are the most common parameters you're using ? I've heard about using Illumina or Sanger quality scale (-Q 64 / -Q 33), Minimal read length (-M), Clipping (-W), quality filtering (-E). Suggestions are very welcomed. -gordon