Blast Tools On Free Public Server

Question: Blast Tools On Free Public Server

6.2 years ago by

We're using the free public Galaxy server (main.g2.bx. psu.edu). We uploaded a genome FASTA sequence via ftp, and want to do BLAST searches (e.g., tblastn) against protein sequences that we've also uploaded to Galaxy, as well as on NCBI. BLAST tools don't show in the tools column, or when entered in the search box. Google searches on 'BLAST in Galaxy' bring up pages on 'wrappers' and xml, and we're but humble biologists. Can anyone please explain (simply, presuming no knowledge of wrappers, perl, python, java, scripts, xml, etc. on our part) how we can do this? Thank you. John D

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modified 6.2 years ago by Peter Cock • 1.4k • written 6.2 years ago by John DeFilippo • 10

6.2 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello John, To use all BLAST+ functions with Galaxy, a local or cloud instance is needed. The public main Galaxy instance does not host tblastn, only megablast (based on blastn) - and only for certain databases. Many biologists prefer using a cloudman instance as much of the set-up is already packaged and it does not require an investment in local hardware/servers/data & tool setup. Details can be found in our wiki at: Cloudman: http://usegalaxy.org/cloud Local instance: http://getgalaxy.org The best mailing list for local or cloud instance support, should you run into issues (or just want to follow the technical threads), is galaxy-dev@bx.psu.edu. http://wiki.g2.bx.psu.edu/Mailing%20Lists Hopefully this helps! Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org

ADD COMMENT • link written 6.2 years ago by Jennifer Hillman Jackson ♦ 25k

6.2 years ago by

Peter Cock • 1.4k

European Union

Peter Cock • 1.4k wrote:

Offering BLAST searches is potentially quite computationally expensive, so for the moment at least the BLAST+ suite is not made available on the public Galaxy hosted by Penn State (with the exception of the megablast function offered with four databases only). The BLAST+ wrappers are available on the Galaxy Tool Shed, and can be installed to any local Galaxy server. They can then be run on your local server (and ideally your local cluster). That's what we do. If you have a Galaxy installation at your institute/department/... ask the local Galaxy administrator about this. Regards, Peter

ToolShed link: http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/

ADD COMMENT • link modified 4.6 years ago • written 6.2 years ago by Peter Cock • 1.4k

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