On Fri, Feb 13, 2015 at 12:08 PM, Michael Thon <mike.t...@gmail.com> wrote:
> I have a new galaxy installation on my server.  I uploaded two fastq files 
> and now I'm trying to run trimmomatic and fastqc. In both cases I am 
> presented with a drop down list of fastq files to select from but the lists 
> are empty.  I double checked the fastq file attributes and they are both set 
> to fastq. Any ideas what's wrong?
>

You probably need to change the format to the more specific
fastqsanger datatype (FASTQ using the Sanger encoding).

It may be time for Galaxy to change their default, since the old
Solexa and Illumina variants are no longer widely used.

> Another question: I have fastq files already on the same server as the galaxy 
> installation.  How can I get them into galaxy? I have not set up ftp yet. Can 
> I move them into a data directory somewhere?

One option is to import them into a library (which can link to the
files rather than coping them). Are you a Galaxy administrator?

Peter
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