On Thu, Sep 15, 2011 at 4:58 PM, Peter Cock <p.j.a.c...@googlemail.com>wrote:

> On Thu, Sep 15, 2011 at 9:32 AM, Timothy Wu <2hug...@gmail.com> wrote:
> >
> > I think I need some kind of "data source" implementation that allow user
> to
> > obtain the data themselves. However with the current tool XML definition,
> I
> > don't know how to have a FTP download tool to download EST data from NCBI
> to
> > Galaxy directly.
>
> Perhaps I have misunderstood you, but I'd just use the provided
> "Upload Data" tool, and paste in the FTP URL for the file, e.g.
> an NCBI FTP URL.
>

I wasn't aware that the Upload data tool could take a FTP URL, so thanks for
letting me know.

Unfortunately that doesn't take a wild card.

I need to have the path specification like this "
ftp://ftp.ncbi.nih.gov/genbank/gbest*.seq.gz"; at the minimum.

Actually my tool is more versatile (though I don't need it for this
particular application).

I could specify

ftp://ftp.ncbi.nih.gov/genomes/*/*/NC_*.fna

and grab all the fasta files for all chromosome of all species under the
genomes directory. I thought it would be a nice tool to have in my galaxy
arsenal.

Timothy
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