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 Ciência ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
