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, dsobral@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 dsobral@igc.gulbenkian.pt =====================================
-- Daniel Sobral, Bioinformatics Unit Instituto Gulbenkian de Ciência