I'm trying to wrap up my own tool in Galaxy. The input to my tool include
the set of EST (such as the entire human collection). I tried using UCSC
genome browser but it doesn't seem to let me download the whole human
collection due to the size of the data.

I tried to implement my own FTP client and try to wrap that up in galaxy. I
intend to have the FTP client download data from NCBI's FTP server directly,
and have the downloaded files as output files to feed back into galaxy. I
intend to make the FTP client somewhat generic, so as not to enforce the
type of files. Though in my case, I would be download gzipped genbank files.

But galaxy support for multiple output files kind of tripped me over. I do
not know exactly what to do, since it looks as if galaxy requires a strict
naming convention for the outputs, according to
case I have is obviously that the number of files would not be known
until run time).

I guess it doesn't really, really matter, if I send those files, whatever
the naming convention are, and fed it to a gzip decompressor (which I am
planning to do a simple wrap up, just to be able to handle my stuff). Then
it should all work out fine.

Alternatively, I can just ask user to download from NCBI ftp themselves,
decompress them, and upload it to galaxy.

What's the best approach here?

And I noticed that file types does not include genbank types nor gzip types.
Is there some generic type I could use? Just Data class?

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