Hi David

Using "Data Libraries", as suggested by Martin is definitely the way to go. Especially if you want to use the files with different tools.

However, if you have a predefined set of tools, you might wanna consider adding an extra tools which reads and process the files, eg: you have your raw fastq files in a central location and you always do the same pre-processing steps. For such a case, I recommend using the "dynamic_options" attribute. This allows you to present a list of files, which you can then select from and do the processing on.

May I refer to a similar question for the details on how to implement this:

http://tinyurl.com/6uom4uo (I can give you more details if interested)

Of course, you can go to the extreme case, and just trigger a copy of the selected file into your history. But this will end up in data duplication and you wanna avoid this.

Regards, Hans-Rudolf

On 11/01/2013 01:46 AM, Martin Čech wrote:

Hello David,

please see whether Data Libraries (http://wiki.galaxyproject.org/Admin/DataLibraries/Libraries) with the file import (http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles) and especially the /Upload files from filesystem paths/ feature do solve your problem. It enables you to work with the datasets while keeping them untouched on the file system.

thank you for using Galaxy!

regards

Martin

On Thu, Oct 31, 2013 at 3:05 PM, David Hoover <hooverdm@helix.nih.gov mailto:hooverdm@helix.nih.gov> wrote:

Is there any desire to create a way in galaxy to browse local
directories on the galaxy server itself?  Not the client machine
running the web browwser, but the machine on which galaxy is
running.  I've created a tool that allows a user to upload a single
file from their own personal directory on the galaxy server into
galaxy directly, without going through Apache.  However, this is
very limiting.  It would be very helpful to be able to browse
directories that are deemed accessible to the galaxy user, and
before I begin trying to develop anything I'd like to know if there
is any support for such a feature.

David Hoover
Helix Systems Staff
National Institutes of Health
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