If you look at the attribute details for one of your fastq files, what does
Galaxy say the filetype is?  You most likely need to flip it from 'fastq'
to 'fastqsanger' so Galaxy will know how to handle the file, it doesn't
automatically detect this.

-Dannon


On Mon, Oct 7, 2013 at 10:38 AM, UMD Bioinformatics <
bioinformatics....@gmail.com> wrote:

> Hello,
> I've installed Galaxy on two separate machines. None of the fastx tools
> recognize my fastq files. They are not appearing in the drop down list on
> Galaxy for input options. I'm getting the same behavior on both machines.
> I've used the tool_shed to install fastx on one machine and I've done it
> manually on the other.
>
> fastx_tools work perfectly from the command line.
>
> Cheers
> Ian
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