Is there anyway to integrate SRA toolkit into Galaxy? I am trying to analyze raw sra files from GEO but it is a lengthy time to download, convert using the tool kit and then re-upload. Is there an easier way to get .sra files into Galaxy?
under "Get Data" EBI SRA you can browse the SRA archive and for many datasets you can download fastq files directly into Galaxy. If that is not working for you can install and test the sra toolkit from Matt Shirley
Would you know how to troubleshoot this tool if it only gives a blank page? Look at this short clip I recorded:
No sorry, but have your tried to use the Tool under Get data from your video?
It is a cookie problem - probably as a result of website changes at the EBI side. If you clear your browser cookies for www.ebi.ac.uk then you will get to see the site - until the next time you follow the galaxy EBI link. I tried in Chrome and Firefox, same behaviour.
A second issue has cropped up too. E.g. on https://www.ebi.ac.uk/ena/data/view/SRR031071 . One must manually select the "NCBI SRA file (galaxy)" field, in order to see it - EVERY TIME one does a search or "Read Files" tab viewing. So not easy to download a batch of SRA entries this way.