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 <hoove...@helix.nih.gov
<mailto:hoove...@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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