On Thu, Sep 15, 2011 at 10:32 AM, Timothy Wu <2hug...@gmail.com> wrote:
> On Thu, Sep 15, 2011 at 4:58 PM, Peter Cock <p.j.a.c...@googlemail.com>
> wrote:
>>
>> 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

That volume of data shouldn't really be uploaded into individual
Galaxy user's histories (not unless you have a Galaxy setup
with an unusually high disk quota per user - lucky you).

This seems ideal for the Galaxy data library functionality, where
the Galaxy admin loads the big data sets and makes them
available to all the Galaxy users (or a subset using access
controls). For the user's history the files are just linked to - so
there is only one copy on disk.
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries

However, we'd also like easy access to (some of) the files on
ftp://ftp.ncbi.nih.gov/genomes/ so a new "NCBI Genomes
FTP-site Data Source Tool" as part of Galaxy would be nice
(like the existing UCSC data source etc).

Peter
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