Hello Mike,

you probably want to set library_import_dir or allow_library_path_paste in
the config.
Details here:
https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles

Martin

On Tue Feb 17 2015 at 11:40:37 PM Michael Thon <mike.t...@gmail.com> wrote:

>
> > On Feb 13, 2015, at 1:35 PM, Peter Cock <p.j.a.c...@googlemail.com>
> wrote:
> >
> > 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
>
> I just tried adding them to a library.  On the library admin page there is
> an option to upload files or to import data from my history.  There is no
> option to link to files on the filesystem.  Does this need to be activated
> in the config somewhere?
> Thanks
>
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