Just an update: when I set it to copy, it works fine as expected.

So I guess the only alternatives alternatives I have are:
- link the file, but as unzipped fastq
- copy the file (which copies the unzipped data to galaxy)

Would be nice to have a way of working with gzipped fastq files, since
most tools now work with them routinely. I'm probably missing something
here?

Thanks,
Daniel

On 12/30/2013 10:18 PM, dsob...@igc.gulbenkian.pt wrote:
> Hello,
>
> I have been using the galaxy API to upload files into a library (using a
> local folder for library import) and running a workflow into a history. I
> have been following the example scripts that come with galaxy.
>
> When I upload a gzipped fastq file, in autodetection mode (linking the
> file and not copying, to be faster), the file is not detected as fastq.
> Even if I explicitly say that it is a fastq, the file is uploaded as a
> fastq but with its contents gzipped (so downstream analysis fail).
>
> Nonetheless, if I do this manually through the interface, the file is
> unzipped correctly.
>
> Any idea how can I upload the gzipped fastq through the API so that it can
> be used properly?
>
> Thank you.
>
> =====================================
> Daniel Sobral
> Next Generation Sequencing Data Analyst
> IGC - Instituto Gulbenkian de Ciencias
> e-mail dsob...@igc.gulbenkian.pt
> =====================================
>


-- 
Daniel Sobral,
Bioinformatics Unit
Instituto Gulbenkian de CiĂȘncia

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